'Sometimes I think it's a shame, when you're reading these horrific novels and then you find they're written by someone who knits and bakes cheesecakes.

And you say to yourself, 'I don't want to think about you writing these books. I don't want these worlds touched by mundane reality!'"

Speaking from his attic office in Dublin, best-selling crime writer John Connolly is talking about how the internet age has changed the immediacy of engagement between readers and authors. He believes it's a wonderful thing that writers can be so accessible to readers, but wonders if sometimes they shouldn't be more mysterious, if occasionally the reality of the writer can intrude on their fiction. Although he admits thriller writer Lee Child might be lucky in that regard: "Lee looks like a slightly older Jack Reacher who's lost a couple of pounds. Which is great!"

Connolly himself bears little resemblance to his own character, the American private detective Charlie Parker. It's not just that Connolly, 45, is originally from Rialto in Dublin, whereas Parker's stomping grounds are the areas around Portland, Maine. After all, Connolly now divides his time between Ireland and the US. It's more that where having a chat with Parker might lead to some heavy duty brooding, Connolly himself is a remarkably effervescent presence. He talks at speed, his brain whirring with rapid-fire connections. He is a reader as much as a writer, and has lost none of the fannish enthusiasm for books that brought him to the writing life in the first place.

It is 15 years now since Connolly's debut, Every Dead Thing. When I met him 10 years ago at a crime fiction convention in Chicago, I had just discovered his work through his third novel, The Killing Kind. I still have nightmares about the villain of the piece: the mysterious Mister Pudd. Since then, I have journeyed constantly with Parker, taking side trips through Connolly's blisteringly funny Young Adult novels, his affecting "fairy tale for adults", The Book Of Lost Things, and science fiction novel, Conquest. This last, written with his partner, Jennifer Ridyard, has brought Connolly again to a wider audience. And on top of all this he still finds time to do the occasional bit of journalism, edit award-winning non-fiction - the fascinating Books To Die For - and hosts a regular music radio show on the digital station, RTE 2XM: From ABC To XTC.

But it's the Parker novels we are here to discuss. They are marketed as crime novels, but include elements of the horror novel, the gothic melodrama and so much more. For someone used to a conservative idea of what a crime novel is or isn't capable of, Connolly succeeds in blowing those expectations out of the water.

The latest in the series, The Wolf In Winter, exposes the dark interior of an American small town, and questions the influence of religion upon the landscape. Its tight plot touches on lost religious cults, mysterious stone carvings, the homeless culture of Portland and Connolly's own, ever deepening supernatural mythology. And it sees the return of a grotesque and mysterious man known as The Collector - my second-favourite Connolly villain.

Given the reactionary nature of genre fiction when he started writing, some people wondered what Connolly was doing writing novels that brought in aspects of other genres. "There was, perhaps, a tacit disapproval of colouring outside the lines," he admits. But he persisted, writing the kind of books that he wanted to read. "Terry Pratchett once said that if you keep bending the rules, eventually people will alter the rules to suit you … They kind of have to accommodate you. Because you're not going away."

But Connolly is still regarded as a crime writer. Despite their blurring of genre boundaries, his books wear the influence of the American mystery with pride. Connolly's greatest inspirations remain James Lee Burke and Ross MacDonald.

From Burke, he takes his ability to disregard the perceived "rules" of writing genre. Of crime writers, he says, "we see ourselves, for good or bad, as part of a continuing tradition. Burke never saw himself as that. Burke's influences were gothic … he hadn't really read a lot of crime fiction. So the kind of rules that tended to apply to crime fiction didn't really apply to him." That use of the Gothic in crime fiction - as well as smooth transitions between first and third person narrative - would become integral to Connolly's own style.

When Connolly talks about MacDonald, you understand the direct influence that the detective novelist had on Connolly's themes and characters. When he talks about "that notion of empathy and compassion. That necessity of acting because to not act … makes you culpable and makes you complicit in what happens", he could easily be talking about his own protagonist. Parker's compulsion to become involved, to right wrongs which perhaps are better left alone, share a great deal in common with MacDonald's own protagonist, Lew Archer.

In The Wolf In Winter, what compels Parker's involvement in the rapidly unfolding events surrounding the mysterious town of Prosperous, Maine, is the apparent suicide of a young homeless man in Portland. While events will lead Parker to a centuries-old religious sect and a dark, possibly supernatural, conspiracy in which he plays an unwitting role, Connolly's evocation of the American landscape is rooted in a recognisable reality. And without that reality, Connolly says, his books simply would not work.

"Because I want to put these slightly odd elements into the books … they work better if the whole world around them seems real. If the whole world is weird, then weirdness doesn't seem that shocking." Connolly's fictional reflection of Maine, and the Portland area in particular, feels concrete. He uses real bars, businesses and landmarks to ground his fiction. Because if people understand the world he writes about to be real, he hopes they'll begin to question, "is this other thing, then, also real?"

This is part of the power of Connolly's writing. Readers are allowed to contemplate something of reality through the escapism of the more fantastic elements, allowing Connolly to ask often complex questions about the world, and the morality of action or inaction.

Of course, infusing his work with moral questions has led to some criticism. "I've been getting a lot of emails over the past year … complaints " - he uses the word hesitantly - "from people who dislike what they feel is the political aspect of my books. I'm always accused of being a liberal. There is a degree of social or political commentary in the books that they don't want from their novels."

And perhaps this is true. As Connolly points out, all novels have a degree of political and social commentary to them, but you rarely complain to the author when you agree with their politics.

But his books are concerned with "justice and compassion and injustice". You can't deal with those themes and not ground them in reality. "As a writer you have a certain duty to address the real world and to engage with it … because we live in the real world." But he understands that literature cannot be entirely non-escapist. "We read to get into another world. But that doesn't mean that it can't have a seriousness, that it can't have moral obligations." The Wolf In Winter deals with the very real moral issue of how we view the homeless. In Portland, Connolly was amazed to see compassionate treatment of the homeless was a real concern for some people, who believed the city was too soft with those fallen on hard times. How could he not comment upon that?

Our conversation winds from these moral imperatives, through to Connolly's "magpie" obsession with history, including the real-life Family of Love who influenced the cult at the heart of The Wolf In Winter, and the mysterious but very real "Church-heads" that feature in his labyrinthine plot. We discuss religion and crime, and why alcoholism features prominently in so many crime novels.

But in the end, we come back to that relationship between readers and authors. For all his earlier joking, he understands the power of engagement. Although some may disagree with his politics, many readers are touched by his writing. "The mere fact that you've written a book and that someone has reached out back to you is really important. There's something quite lovely about that. You think: that's why I'm doing this."

The Wolf In Winter is published by Hodder & Stoughton, £14.99