Bill Bailey is not exactly what he seems. He's a cuddly hippy with an acid tongue; a light entertainer who once performed for the Workers Revolutionary Party; a panel-show regular who's had his fill of panel shows; an arena-filling comedian who reckons that most people have no idea who he is. Judge him by his rocker's hair, his psychedelic posters and his show titles - Cosmic Jam, Bewilderness, Part Troll - and you'd think he's some reefer-damaged dropout. Hear his stand-up, and his manner is more Hancock than Hawkwind: “I'm English,” he once announced, “and as such I crave disappointment.”

He began a West End run of his latest show, Tinselworm, last night. He plays a scat-jazz rejig of the death march from Star Wars. He sets Kant's categorical imperative to the Match of the Day theme. He raps at a supermarket chain for asking him to be in its adverts. A 43-year-old white beardy bloke, co-opting hip-hop to moan about Asda? “I though it had a sort of poetic incongruity about it,” he chuckles.

And that sense of poetic incongruity is the defining feature of a man who one minute is outgunning second-string pop stars on Never Mind the Buzzcocks, the next is staging Pinter sketches, and a guide to the orchestra at the Albert Hall.

Bailey is angrier and more interesting than his cartoon image. Is he misunderstood? He certainly hopes so, he says cheerily, nursing a pot of mint tea at a café near his home in Hammersmith, West London. “Maybe it is just a childish thrill, but I think there is so much about popular culture that is so readily understandable, so readily packageable: oh, that's him, he does that. It's easy and you don't have to think too much about it. And I resist that.”

So when Asda came calling, asking him to be part of its series of adverts in which celebrities dress up as Asda assistants, he wasn't just resistant. He was offended. He took it as a suggestion that his relationship with his audience, something he'd built up over 20 years, was just another commodity to be bought or sold.

“I know people aren't really bothered by that sort of thing,” he says, “they just think: ‘Oh he's that bloke, he was quite funny in that ad.' But I don't think that. I see the ad and I think: ‘What the hell are you doing? Have you not got enough money? Why are you taking the Wal-Mart [Asda's parent company] dollar? Have you seen Wal-Mart - The High Cost of Low Price, the documentary about Wal-Mart? Watch that and then tell me you want to do the ad.'”

Bailey is crazily bright, musically gifted (he has perfect pitch) and endearingly self-deprecating (a quarter of the population has perfect pitch, he insists). He plies his vulnerability with the steady charm of someone who, secretly, is comfortable in his own skin. He's also a rare example of a star comedian who's equally interested in popular culture and intellectual pursuits.

He spent the day before we meet, he says, “trying to get my head round the post-Structuralists, thinking: ‘Come on, there's something here!'” So he goes through Derrida and Baudrillard with a highlighter pen, looking for gags? Not entirely. “If I'm really honest,” he says, “I'm trying to look for meaning in things. And philosophers, that's their job. So anyone that is doing that I'm going to give the time of day to, even though it might just be pretentious bollocks.”

He was born Mark Bailey, but at school he got the nickname “Bill” (after the song Won't You Come Home Bill Bailey) and it stuck. His mother, a nurse, never got used to the name. “People would ring asking for Bill. She'd say: ‘There's no Bill here. Would you like to speak to Mark?'” His father, a GP, now calls him Bill.

He started playing the piano as soon as he could reach the keys, then taught himself the guitar. At his boys' school, King Edward's in Bath, he was a bit of a prodigy. But he traces his distrust of authority to his experiences in the sixth form. Starring in a production of Brecht's The Resistible Rise of Arturo Ui, for which he dyed his hair black - “It was the only time my Mum said my hair looked nice. I said, ‘Mum, I'm supposed to look like Hitler!'” - he found teachers scrapping over him. He realised that teachers had “a rather childish ownership of how well you do”.

Bailey went to university in London to study English and drama. But he spent his time in a French-speaking theatre company, putting on A-level texts for schools. “It was such a blast. And I thought, this is much more fun than sitting in lectures, listening to iambic pentameters.”

He left university after the first year, “by mutual consent”, started doing stand-up and appeared in the odd play - including Printers, a play about the print unions written by Corin Redgrave for the Workers Revolutionary Party. Was he WRP himself? “I never joined the party, but I joined in. I enjoyed it. But I stopped short of the idea of England being ready for revolution. I was only 21, but I could see that that's not going to happen, is it, if the snooker's on?”

Slowly, Bailey's musical comedy act the Rubber Bishops started to get work. From 1988 to 1994, he and Martin Stubbs played at clubs all around Britain and Ireland. “It felt like I'd found my niche,” he says, “my world.” But they were doing “ludicrous amounts of gigs”. Once, in the summer of 1994, they did four gigs in one night in three cities, ending up in Birmingham at 3.30am playing a student ball sponsored by ProPlus. “It was light when we came out, and I thought, it can't go on like this.”

Bailey made his Edinburgh solo debut in 1995. He crammed in all his hobby horses - music, politics, sci-fi, telly, intellectualism - because he didn't know how else to keep people interested for a whole hour. After ten years, he was an overnight success. The next year he was nominated for a Perrier award, losing to Dylan Moran, who later gave him his breakthrough sitcom role as Manny in Black Books.

He married his wife, Kristin (they have a son, Dax, 4) and his career blossomed. Even so, never mind 100 episodes of Never Mind the Buzzcocks, he still sees himself as a cult act. “I think I've got a small audience. Lots of people come to my shows but it's not a mainstream audience. If I walk down the street and there's a group of people, maybe one of them will go: ‘That's Bill Bailey.' Four of them go: ‘Who?'”

He has just decided to go cold turkey on the lucrative panel shows, the erudite QI included. “I must admit,” he says, “I've never, ever felt comfortable doing them. I enjoy them, but I've never felt that it's my niche. I'm quite low-status, and those things are very competitive, you have to be quite ruthless, and that's not really me at all. Yet if you're not like that, you just get buffeted around.” And for a man with perfect pitch, it must have been hard to endure some of the singing on Buzzcocks? “Yeah, you think: ‘I can't stand here with some gormless indie twerp humming the intro to In The Air Tonight to some daytime TV presenter... this is my life!'”

His live shows are his metier. But they aren't without their frustrations either. Last year, he staged Pinter's People, a production of Harold Pinter's sketches, in the West End. But the daily critics couldn't see any poeticism in this incongruous cast of comics' “coarse” approach. Bailey is still bruised by it all. “Even now,” he says, “objectively, calmly, I do think it was unfair. It sounded like a bunch of dyspeptic colonels being told that there was jazz being played in the club bar. There was a harrumphing tone to it.” Before the far more positive Sunday reviews came out, Pinter rang Bailey to commiserate. “He said it was totally undeserved and they'd missed the whole point of the exercise.”

Next year Bailey will make another of his television wildlife series, then do a stage-show guide to Alfred Wallace - the amateur botanist who came up with the theory of evolution at the same time as Darwin, but who is unlikely to get much other coverage in the bicentenary year of the founding father of natural selection. It's got a bit of everything Bill Bailey in it - music, jokes, scholarship, drawings of funny-looking creatures, tackling injustice.

First, there's a final fling for Tinselworm - a smaller version of a show that toured Britain last winter. There'll be more music, less technology. More room for a few poetically incongruous digs at capitalism at its least charming. “You have to pick your targets,” he says. “And I've realised that, consciously or unconsciously, I tend to target multinational companies! The world's richest banks, the world's richest retailers, people who aren't vulnerable. Because I think, of anyone, you can take this, me, some beardy bloke, shaking a fist at you.

“That was the thing about the whole Russell Brand and Jonathan Ross affair. It was just the wrong targets.” They mocked the weak? “They mocked the weak. You have got to aim a bit higher than that.”

Tinselworm is at the Gielgud, W1 (08444 825130; www.billbailey.co.uk), to Dec 22

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