The former Beatle was given the "songwriters' songwriter" at the annual awards event in recognition of his half century as a hitmaker.
Sir Paul, who closed the Olympics opening ceremony last year, was given a standing ovation by guests at London's 02 Academy in Brixton.
The former member of the "Fab Four" told the crowd: "The great thing about songwriting is that you don't know how you do it, so you can't talk about it."
He was presented with the prize by Blur and Gorillaz star Damon Albarn who said: "What can I say other I love him like millions and millions of other people. He's a lovely spirit and a beautiful human being."
The Beatles first headlined the NME Pollwinners Party almost 50 years ago, back in April 1964, as Beatlemania reached fever pitch across the UK.
Fast forward to the turn of the millennium and Sir Paul was a guest of honour at the NME awards, picking up a gong on behalf of the Beatles who were voted the Best Band Ever.
The biggest winners tonight were Arctic Monkeys who picked up five prizes including best album for AM, best live band and best British band.
It comes on the back of a double win last week at the Brit Awards for the quartet.
"Hard Out Here" singer Lily Allen won best solo artist, which the mum-of-two said was "kind of dumb" as she was in the same category as David Bowie and Jake Bugg.
Scottish band Belle & Sebastian collected the outstanding contribution to music prize with guitarist Stevie Jackson playfully mocking David Bowie's Brit Awards plea for Scotland to remain in the UK.
He joked: "England stay with us - at least just for a night. And if we do leave you, let's stay friends."
Full list of winners
- Godlike Genius - Blondie
- Songwriters' Songwriter - Sir Paul McCartney
- Award For Innovation - Damon Albarn
- Outstanding Contribution to Music Award - Belle & Sebastian
- Best British Band - Arctic Monkeys
- Best International Band - Haim
- Best Solo Artist - Lily Allen
- Best New Band - Drenge
- Best Live Band - Arctic Monkeys
- Best Album - Arctic Monkeys, AM
- Best Track - Disclosure, White Noise
- Best Festival - Glastonbury
- Best Book - Morrissey, Autobiography
- Music Moment Of The Year - Noel and Damon come together for Teenage Cancer Trust
- Worst Band - The 1975
- Best Fan Community - Arctic Monkeys
- Hero Of The Year - Alex Turner
- Villain Of The Year - Harry Styles