It means the problem is you. Or rather, the problem is his problem with you (ie, his deep and powerful psychological desire to no longer date you).

This is one of those questions I almost didn't want to spend time answering, because I'm astounded that people exist who still can't decode such an obvious and douchey message from a guy. But for the same reason, I feel it's my duty to say yet again:

No one says "it's not you, it's me" seriously. It's become an accepted fact that anyone saying that means the exact opposite, like how tiny candy bars are called "fun sized," when we all know that clearly, the most fun size a candy bar could be would be large enough for you to live inside of.

Thankfully, people most often use this phrase ironically, as a joke. I'll sometimes whip it out during a stand-up routine and just watch the laughter roll in. It's what comedians call "a freebie" (others include loudly farting into the microphone and any mention of sea monkeys).

And if your guy is the one-in-a-million guy who actually has a deeply tortured soul and is just trying to distance himself from you so you won't get hurt, then...well, then nothing. The end result is the same. "It's not you, it's me," is the sound of your relationship flatlining, because either this guy is secretly in the mafia or he's secretly an asshole (an an uninventive one at that).