Kim Kardashian had a gun held to her head while she was in Uganda with Kanye West ... and, according to her biographer, Ye was the reason it happened.

Jonathan Van Meter -- a well-respected entertainment journalist who penned Kim K's new biography, "Citizen Kim: The Woman Who Created the Future" -- relays the story told to him by Farnaz Farjam ... a TV exec who worked as a producer on "Keeping Up with the Kardashians" back in the day -- and he says Farnaz told him the 2018 trip proved how bad Kim and Ye's relationship really was.

He says the trouble popped off when a paranoid Kanye -- convinced someone was trying to drug him -- talked local cops into searching every room at the resort where they were staying

Van Meter writes that at a point, "One of the policemen had a gun to Kim’s head."

Obviously, Kim survived, and photos of the trip make it seem like the pair were a happy couple ... though they would divorce just a few years later.

Van Meter didn't interview Ye for the book -- saying he didn't feel it would be fair to do so while Kanye's dealing with his numerous mental health issues. He did talk to Kim all about Kanye, though ... and she told him she still worries about her ex.

She says she tries to make him seem like a good guy to their 4 children ... though it's hard when he's not around much.