The former Libertines star has opened up about his romance with the Rehab hitmaker in an interview with Britain's Mail On Sunday newspaper.
He says, "This is difficult for me to admit. But, yes, it's true. Amy and I were lovers. I loved her then and, well, I still do today."
However, Doherty claims the relationship was tumultuous, adding: "Towards the end, as only lovers can, she became quite mean and cruel to me. She didn't suffer fools... and believe me, she had a mean right hook."
Detailing their time together, Doherty remembers how Winehouse hardly ate and how she was always watched over by two hulking bodyguards.
He recalls, "She had such a big heart but she was physically small and increasingly frail and I never once saw her eat anything solid, just milkshakes.
"She came back to my hotel after the Libertines reunion warm-up gig at the Forum in Kentish Town (London) in August 2010, but she had two huge bouncers with her. I told her she would have to leave them outside in the corridor, but she looked at me despairingly and said, 'I can't!'"
Doherty has now penned a new track in honour of his former lover, but he confesses he is still struggling to come to terms with her death: "I've written a song about Amy for my new album, called Flags From The Old Regime. I've never done a song like it - it's very slow and melodic. I've also got lots of lovely video footage of me and her just being together. But I haven't been able to watch it yet."
Winehouse died from alcohol poisoning in July, 2011.