Sean McAllister's A Syrian Love Story won the grand jury award at Sheffield Doc/Fest at a ceremony on Wednesday.
His film follows a family as they flee the country during the civil war.
McAllister was detained in Damascus in 2011 and has spoken about how he heard activists being beaten and tortured before his release a week later.
His film depicts two opponents to the Syrian regime who fell in love while communicating through a tiny hole in a wall between neighbouring prison cells 15 years ago.
After being released, they got married and started a family but moved to Lebanon and then France after the Syrian uprising began in 2011.
McAllister, from Hull, said he wanted the film to provide viewers with "time to be with Syrians who laugh and cry and are not just dead news items".
Sheffield Doc/Fest grand jury member Ruby Chen said: "The jury were enamoured by this Bergmanesque portrait of a relationship and love, taking place against an ever-changing and tumultuous backdrop."
A British film-maker who was arrested while making a feature about a Syrian family has won the top award at the UK's leading documentary festival.