Lee began his film career in 1977 and in 1985 he started his prolific collaboration with Taiwanese filmmaker Hou Hsiao-hsien.

A member of the Academy of Motion Picture Arts and Sciences, Lee was honored with nominations by the American Society of Cinematographers for its 2014 First Annual Spotlight Award for Best Cinematography for his work on the 2012 film Renoir and by the French Academy of Cinema Arts for a César Award for Best Cinematography in 2014 also for the film Renoir.

In 2009, Taiwanese director Chiang Hsiu-chiung and Kwan Pun Leung made a documentary about Lee entitled Let The Wind Carry Me.

Also in 2009, a book of Lee's photography entitled A Poet of Light and Shadow was published.

In November 2021, he succeeded director Ang Lee as head of the Taipei Golden Horse Film Festival Executive Committee.