Goum Ian Iskandar (left) is the youngest Golden Horse recipient
Chan was named best director and China's Zhou Xun was named best actress. The film also won best cinematography and best song.
But After This Our Exile caused the biggest surprise by scooping best film.
It also made nine-year-old Goum Ian Iskandar the youngest Golden Horse winner for best supporting actor.
The film was honoured again when Hong Kong actor and singer Aaron Kwok picked up his second consecutive award for best actor for his portrayal of a single and abusive father.
"The movie is a huge challenge for me... but I never thought I could win (best actor) again," he said at the ceremony in the Taiwanese capital, Taipei.
The 43rd award ceremony was dogged by controversy in the run-up to the event.
Two nominated films pulled out of the competition.
Director Tsai Ming Liang, who is Malaysian-born but a Taiwan resident, withdrew his film I Don't Want to Sleep Alone, upset by comments from jury members that it was too self-indulgent and failed to engage audiences.
And The Go Master, a film by Chinese director Tianzhuang Zhuang, was also abruptly pulled with no official explanation given.Other winners included Hong Kong's Nikki Shie, who won best supporting actress for her role in the film Reflections.
I would have done the same thing Tsai Ming Liang did. The juries in Taiwan are not humble and lack experiences in judging films. First off, there's barely a film industry in Taiwan. Therefore based on what do these Taiwanese judges have for the filmmakers to respect. And the remarks they made were totally inappropriate.