Kiwi Chow's "Revolution of Our Times" was named best documentary, prompting a long round of applause and shouts of support for Hong Kong from audience members at the glitzy event in Taipei.
Chow, who sent a pre-recorded message from Hong Kong expressing thanks for the award, dedicated the film to Hong Kong's people, saying he hoped it would bring them some comfort.
"I cried a lot when I produced this film; several times I comforted myself with this film, to express my anger, hatred, to face my fear and trauma," he said, his voice cracking with emotion.
Native Hongkonger Chow's film follows several protesters and documents clashes with police during the 2019 demonstrations, and he has previously told Reuters he hoped the documentary would help the pro-democracy movement live on.
It was shown at this year's Cannes Film Festival in a surprise addition to the line-up.
China introduced a sweeping national security law for Hong Kong over a year ago to crack down on what it deems subversion, secessionism, terrorism and collusion with foreign forces.
Since then, cinemas, universities and art galleries have cancelled screenings or exhibitions of protest-related works.
The protesters have won broad support and sympathy in democratically-ruled Taiwan.
China, which claims Taiwan as its own territory, in 2019 blocked the country's movie industry from participating in the Golden Horse Awards, which were founded in 1962 and take place annually in Taiwan.
Beijing's move followed uproar in 2018 in China and among Chinese stars at the awards ceremony after Taiwanese director Fu Yue made comments in support of Taiwan's formal independence, a red line for Beijing.