When journalists used to visit Philip Pullman, they were invited to a shed in his back garden in suburban Oxford. For years he had written in this shack-out-the-back to escape the sound of his son's violin-playing. "His playing was fine," says Pullman, "but I need to hear the rhythm of my next sentence in my head before I write it. I can stand traffic, screaming kids, but not the competition of music." The remark confirms Pullman's appealing niceness (not for a moment would he suggest his son's fiddling was anything but enchanting) as well as his writerly fastidiousness.

Pullman, 58, no longer owns the shed where he wrote the famous trilogy His Dark Materials between 1993 and 2000, nor the modest Oxford house where he and his wife of 34 years, Jude, raised their two sons. His fortunes have altered dramatically. His trilogy, whose popularity proves there are many children out there who like to be intellectually challenged in their reading, has sold 7m copies in 38 languages. There has also been a sellout stage adaptation directed by Nicholas Hytner at the National Theatre (due for a second run from later this month), and a three-part movie series is being written by Sir Tom Stoppard, to be produced by the film company that made the adaptations of The Lord of the Rings. All of which amounts to what publishers call "a second and a third bite of the cherry". Pullman is one of the most successful authors of the new century. And his fame and fortune are certain to go on rocketing. The question is not just how sudden wealth has altered his character and lifestyle, but how it has affected his powerful imagination and the rhythm of his writing.

Pullman, who is about to publish a new children's book and is planning a top-secret stand-alone novel about his Dark Materials heroine, Lyra, has recently relocated. He has bought a detached, modernised 16th-century farmhouse in the rolling countryside of well-heeled Cumnor, just 10 minutes by car from Oxford station. A new Mercedes E320 estate stands on the secluded brick-paved driveway.

He greets me at the door. Tall, bespectacled, fleshy, although in reasonably good shape, he has the self-effacing air of an old-fashioned university don. As he speaks, there is an impression of the musical clarity of a practised storyteller; a barely perceptible Welsh lilt. Every so often, though, his jaw hardens and the large pale-blue eyes are no longer smiling, indicating a potential for fiery antagonism. His shirt and trousers are workman blue, but his cardinal red socks signal a flash of subversive panache. He takes me to the kitchen - expanses of terracotta tiles, downlighting, new designer units, and a resplendent cream four-oven Aga. "We've been bending this house to our will," he tells me.

While he makes a cafetiere of very black coffee, he establishes his authorial credentials. Pullman has been publishing children's stories since he was 25, but it took him three decades to be noticed and to make money. All that time, struggling on modest salaries in schools and latterly at a teacher-training college, he was paying tithes in abundance to his craft. Yet he does not give the least impression of injured merit. He believes, in fact, that his current burst of success is due in large measure to luck, not least his publisher's decision to release the His Dark Materials trilogy as children's books rather than adult fantasy. "Had I been classed an adult-fantasy writer," he says, "the books would never have flown off the shelves. Nothing succeeds like a book recommended by your children."

Has success disrupted his writing? Amid the pressure-cooker publicity of the past two years ("It is so difficult," he says, "to cut oneself off nowadays from endless distractions and travel"), Pullman has completed The Scarecrow and His Servant, a 200-page adventure for children, published next month. It is not so much to keep the cash flowing as to satisfy his addiction to writing stories. It will delight his fans for its breathless pace and inventiveness, as well as the humour and decent humanity of the central characters (albeit one is an assembly of straw and wood, with a turnip for a head and a pea for a brain). It is tight, and not remotely on the scale or complexity of His Dark Materials; it also has illustrations by Peter Bailey, reminiscent of Ardizzone's drawings. But the new work, which features a wise servant and a foolish if well-meaning master (the scarecrow), is sustained by a hilarious jumble of literary allusions: Frankenstein meets Don Quixote meets Mr Micawber meets Jeeves meets Dr Watson and Sherlock Holmes meets The Name of the Rose meets Treasure Island. My six-year-old granddaughter couldn't get enough of it; nor could I. As for reading levels, on our third session she snatched the book from me and started to read fluently by herself.

Amid a catalogue of themes in the book is the notion of continuity of personality, despite the constant replacement of the parts. The scarecrow's body is constantly being lost and replaced, attacked by termites, lopped and recycled. "I'm fascinated," says Pullman, "by the idea of permanence and change, like old ships that get re-clad till there's nothing left of the original, and yet stay the same ship." His conversation never strays far from such metaphysical questions.

On the kitchen table, which, he says, he made with his own hands, lie dog-eared copies of the New Scientist and the Scientific American. Pullman is an aficionado of the weird realms of physics, from which his imagination has derived the notion that our existence is played out in parallel universes. In these "other worlds", circumstances can be familiar but dramatically different. The scientific reference marks the contrast between his peculiar vision of the possible, however remote, and "mere" magic and witchcraft - of J K Rowling, for example - which demands total suspension of disbelief.

In Northern Lights, the first of the His Dark Materials trilogy, Pullman conceives of an alternative but contemporary Oxford in which travel technology has not got beyond steam and the airship, and where human beings are accompanied by individual soul-mate familiars in the form of protean animals known as daemons: monkeys, birds, snow leopards, reptiles, moths. It is also a world in which the fall of man, as told in the Bible, represents human emancipation rather than a moral catastrophe and hereditary guilt. Pullman's preoccupation in the trilogy is nothing less than "man's first disobedience and the fruit". In his reprise of Paradise Lost, original sin is a lie, and God is an ancient fallen angel who has perpetrated a creationist con on the human race, wickedly exploited by a viciously inquisitional church. As the trilogy develops, the central teenage character, Lyra, emerges as a second Eve. In a quest that takes in the literal death of "God", who is no more than a wizened, foetus-like invalid, Lyra releases human beings from attachment to the afterlife. Meanwhile, Will, the novel's hero, who becomes Lyra's companion, enables her to pursue her quest to its ultimate bittersweet consummation with the aid of a "subtle knife" (based on the laws of quantum physics), which allows him to cut windows into parallel worlds. The finale is the toppling of the kingdom of heaven and the establishment of a celestial atheistic republic on Earth. Small wonder the Christian right in America are out for his blood.

Pullman's imagination is foundry-like in its sparky energy. He is fascinated by the drama of ideas. He sees a link between the way a writer can hold a repertoire of words, images, metaphors, in suspension before final commitment on the page, and the mysteries of quantum physics, in which phenomena appear to exist in a state of unrealised potency until the researcher brings them into actuality by a specific measurement. He refers frequently to the famous "Schršdinger's cat" conundrum, and what physicists call the "collapse of the wave function", in which a cat in a sealed box can be understood to be both alive and dead under certain abstruse quantum physical conditions.

The strange ambience of science-based paradoxes seems to spill into his everyday life. As he walks through the house, two sibling pugs are glued to his heels. The one called Hogarth is charcoal-black, a contemplative podge that looks out upon the world with stupefied wonder. The other, Nellie, is stone-coloured, abrasive and jittery. Could these be Pullman's twin but contradictory daemons? The pugs, one gentle-eyed and adoring, the other pop-eyed with indignation, are reminiscent of the diametrically opposed judgments that have dogged Pullman's work, outlandishly exemplified by the Hitchens siblings. Christopher Hitchens, the left-leaning Washington journalist, has hailed Pullman a literary genius and a salutary influence on the young; whereas his right-wing brother, Peter, has denounced him as the "most dangerous man in England" for his denial of God and Christianity. The contradictions continue to rage. While the archbishop Rowan Williams has advocated the teaching of Pullman in schools for the profound ethical questions he raises, The Catholic Herald would have him and his works burnt at the stake for corrupting youth.

Pullman leads me through a door marked "The Way to the Southseas" and into his work room, an extension at the back of the house. The space is a luxurious alternative to the old garden shed. Bright, cool, book-lined, it has a raised desk-cum-workbench at one end: he writes with a pen and copies onto a PC. Jostling spines with collections of children's books are the works of fashionable scientific theorists: Daniel Dennett on Darwin, Steven Pinker on consciousness, Steven Weinberg on theories of everything, Stephen Hawking on black holes, Richard Dawkins on evolution, David Deutsch on styles of explanation. In the middle of the room stands a carpenter's vice and various tools. He loves handling, carving, chipping at wood; between writing and plundering the mysteries of science he is sculpting the head for a rocking horse he is making for his granddaughters.

The swap of Pullman's tool shed for a shedload of money is an unavoidable topic. Pullman, it seems to me, is not entirely comfortable with his new-found wealth; or, more accurately, with temptations to extravagance. As I admired his car, he said a trifle hastily: "Yes. But it's diesel: 50 miles to the gallon on the long trip." As for the Aga: "Mmm... but I can't help worrying whether it contributes to global warming." He ducks his head uneasily with the irony of it all. Then he issues a disclaimer, for which he is indebted, he says, to Clive James: "You know, there are two kinds of riches: not as much as you think; and more than you can possibly imagine." His fortune, he assures me with an amiable chuckle, is more the former than the latter, and there are taxes to be paid. All the same, at 10% of the gross, we are perhaps talking £5m after tax. And it's far from over. "What difference has it made to my life?" he asks. "Well, I don't have to think before buying a book. I can buy nice wood for carving, and I'm no longer worried about security in old age." But there is another difference upon which his appealing modesty is not inclined to enlarge. He has been donating money to the victims of torture.

The fact that he has not used his money to leave the country and escape taxes, or even to leave Oxford, is intriguing and instructive. Pullman was born in 1946 in Norwich, the son of an RAF officer. When he was seven his father was killed fighting the Mau Mau in Kenya. His mother remarried and they moved to Australia. But he returned to England to attend prep school. He was looked after by a parson grandfather named the Rev Sidney Merrifield during the holidays in Norfolk, where he became conversant with, if not converted to, the realms of Christian belief. The family moved again, to Wales, where he attended a state secondary school in Harlech.

In 1965, aged 19, Pullman won a place at Oxford to read English language and literature. Oxford, it seems, became his literal and spiritual home. He was not, he tells me, a brilliant scholar Ð "just glib and very plausible". His Oxford tutor at Exeter College was Jonathan Wordsworth, direct descendant of the poet, and typical of the more patrician-sounding Eng-lit mentors of the era, which included Lord David Cecil, Christopher Tolkien and John Bayley (Iris Murdoch's husband). There was something peculiarly stimulating about Mr Wordsworth's influence. Among his students were the future poet Craig Raine and future novelists James Hamilton-Patterson, Jeanette Winterson and Martin Amis. Hamilton-Patterson hung around in Oxford for years, and Raine has never left. Amis, though, has always been adamant about the deleterious effects on a writer's life of remaining in the lap of alma mater. "If you want to grow up you've got to quit the nursery!" he used to tell writing contemporaries who lingered: like Raine, James Fenton, Ian McEwan and A N Wilson. Pullman says reading English had not the slightest influence on his writing career. And he insists that he did effectively leave Oxford, for a time at least. "I went to London and worked at Moss Bros in Covent Garden for 18 months, then in a bookshop off Charing Cross Road." But after studying for a postgraduate certificate in education he was back again. He taught unruly kids out on the council estates of Blackbird Leys before taking a job at a middle school in the city, where he wrote and directed eight school plays to appeal to pupils and parents. Later he lectured in English at Oxford's Westminster College. "I wasn't beguiled by the Oxford of my university days," he says. "As a student I went through the place like a neutrino. I never went to lectures because I could never find the lecture halls. I spent my time painting pictures, drinking and reading trashy thrillers."

Like a neutrino? Had Oxford English truly affected you, I playfully suggest, you might have said you passed through like the bird in the Anglo-Saxon feasting hall: from the darkness into the light and noise, then out again. Pullman's face clouds a little. "Yes, of course, Beowulf! But I can do science and Beowulf." I refrain from telling him that the bird and banqueting hall come not from Beowulf but from Bede; but the slip confirms a striking aspect of Pullman's acquaintance with a huge circuit of ideas and reading.

As we talk, he keeps an impressive number of balls in the air: the influence on his new book of Tiepolo's cartoons, the narratives of Plautus, the writing style of P G Wodehouse, the inventiveness of Italo Calvino; the possibility that the brain is a quantum computer and that universes spawn baby universes; the benefits and drawbacks of contemporary literary theory. Yet his citations are not so much recondite as exploitable stimulants for his dynamic imagination.

We've agreed that the queasy problem of the proliferation of new scientific theories is that science does not speak with one unerring voice: the conclusions of science, as they apply to human nature and society, represent a babble of contradiction. I ask him: how then does the ill-equipped non-scientist choose between contradictory, competing scientific theories? "Oh, but I'm not looking for ultimate truth from science," says Pullman. "I plunder scientific theories like a magpie."

A current preoccupation of his is the issue of "Platonism". "We have a sense of discovery of a spiritual world, or a world of forms, outside ourselves. Take mathematics: do we construct maths within our minds, or does it exist in a parallel world that we discover rather than invent? When I write I so often have a sense that I am discovering rather than making something up."

Such is the theme of my conversation with Pullman, as he drives us in his new Mercedes E320 diesel into the bosom of Oxford to Walton Street, where he has booked a table at the Loch Fyne restaurant. As he quaffs an order of oysters, he expands on the theme of the soul of the writer. "Is it not amazing that there's such a thing as the authorial imagination, that can flit about the world, that can enter the minds of men, women, children and animals; that can glide through forests, across and beneath oceans, and spring across mountain tops with consummate ease? There is no species or creature in the universe that can do such a thing."

The conversation thus turns to the artistic ruminations of James Joyce and the blasphemous notion of the artist as a rival of the "God of the creation" dwelling "within or behind or beyond or above his handiwork, invisible, refined out of existence, paring his fingernails". Then he hastens to tell me about the profound influence on his work of the story of God and the creation of humankind in Paradise Lost. It was his sixth-form teacher, Edith Jones, who introduced him to Milton's great epic, a book that set his imagination on fire. It would become the catalyst (and title's origin) of His Dark Materials. Why?

Here is Satan, he declares, having lost the war against the Almighty and the angelic legions led by Michael the archangel: "Into this wild abyss, The womb of nature and perhaps her grave, Of neither sea, nor shore, nor air, nor fire, but all these in their pregnant causes mixed, Confusedly, and which thus must ever fight, Unless the almighty maker them ordain, His dark materials to create more worlds..."

It would take him years to see connections between Milton's dark materials, the cosmological mysteries of dark matter, and the proliferating universes of mind, soul and the universe suggested by new physics. But his schoolteacher Miss Jones, still alive and hale in her eighties, he tells me, was also a crucial influence when it came to the rhythm and sounds of writing and reading. "She had the clear-eyed, old-fashioned idea," he says, "that we'd get a good sense of the poem if, before we did anything else, we read it aloud."

And so, the stimulus of Milton, Pullman assures me, was not a result of a privileged Oxford University education but of a Welsh state school. Yet he has inherited in good measure that special genius of Oxford, his chosen home, and its inspiration of literature appealing to children and adults. There was Lewis Carroll, pseudonym for the Oxford mathematician Charles Lutwidge Dodgson, who gave us Alice in Wonderland; then there was C S Lewis, the theologically tortured Ulsterman and fellow of Magdalen College, who enchanted generations of children with his Narnia stories; then there was J R R Tolkien, an Oxford professor of old Norse and Anglo-Saxon, who produced The Lord of the Rings. Pullman's face darkens with mention of C S Lewis. Pullman despises Lewis's premise that would have children trapped in a false world of innocence. He believes that books for children should be about struggles for maturity: growing up.

And with the coffee I am treated to a combative side of Pullman I had suspected lurked beneath his benign surface but never thought to witness. Suddenly the former schoolmaster erupts against the "lunacy" of Sats tests in early-years education, and the publishing of children's books that are written not as authentic narratives but merely to exercise literacy skills in the damnable "literacy hour".

"It seems to me significant," rages Pullman, "that George W Bush was depicted endorsing in a Florida classroom a book of stultifying stupidity entitled My Pet Goat while the 9/11 attacks were in progress." Pullman's anger against the war in Iraq, his loathing of the American administration, his disillusionment with Tony Blair, come together like an exploding fireworks factory in his furious rejection of the government's education policies. Emboldened by his success as a writer, he tells me, he sought and achieved an interview with Charles Clarke, the education secretary. "He listened sympathetically," he tells me, his eyes blazing, "but the problem lies with that specious chap David Miliband, who is responsible for schools."

I feel, as I call for the bill, that I am encountering a meltdown of the real core of Pullman's emotions. Reading his new book, The Scarecrow and His Servant, there is a plethora of politics just below the surface adventures of the romping, picaresque story: the destruction of bird species; the power of multinationals; the greed of the mafia; the poisoning of the planet. I suspect that children are likely to respond sympathetically to these issues even if they might seem routinely politically correct in isolation from his narrative. It's in the way he tells it, of course!

Philip Pullman is angry about many things. But the chief focus of his fury is early-years education in Britain. "I hate the way this jargon-ridden government talks about delivering a curriculum to schools. I loathe the way in which Blair and co spend all their time attempting to placate the readers of the Daily Mail..."

Pullman has much in common with those Oxford predecessors, Carroll and Lewis and Tolkien, who, like him, took children, and adults, down holes and through wardrobes into parallel worlds of the imagination. But he differs from them in his preference for science-based wonder, as opposed to the supernatural and witchcraft. He differs from them, moreover, in his passionate portrayal of dilemmas, choices, challenges and threats that occur in the cold light of everyday reality rather than the realms of fantasy. He wants to lead his readers towards maturity, not back to a childhood of arrested development.

Meanwhile he identifies the true enemy of our children's imaginative promise not in the stock social ills of television, drugs, crime and deprivation, but in the rigid, over-tested, over-structured "sterility of a literacy curriculum that is short-changing a whole generation of our children"

The Scarecrow and His Servant, by Philip Pullman (Random House, £10.99), is published on November 4. To order a copy at the Books First price of £8.79 plus £99p postage and packing, tel: 0870 1658585