The NTMoFA has primarily focused its research work on the fine arts of Taiwan. The Museum's research team sets the agenda and direction for the permanent exhibitions. It is also responsible for publishing The Journal of National Taiwan Museum of Fine Arts, conference papers, as well as research-based book series including A Comprehensive Collection of Taiwan's Regional Art History, Criticism on Taiwanese Fine Arts: the Complete Collection, The Essence of Taiwanese Fine Arts, The Great Masters of Taiwanese Art, and Forty Years of Taiwanese Fine Art, among others. Besides, the NTMoFA's research team often collaborates with university art courses in developing research programs, organizing conferences, or publishing theses on themes relating to fine arts of Taiwan, with an emphasis on the inherent subjectivity of Taiwanese art. From 2007 onward, the NTMoFA has organized permanent exhibitions on significant works from the NTMoFA's permanent collection. An all-encompassing artistic and educational institution, the NTMoFA serves multiple functions as an art collector, exhibition organizer and learning resource provider.

In light of the fact that the NTMoFA's main areas of research have expanded to photography, multimedia arts and all forms of filmmaking, and that contemporary filmmaking in Taiwan is now intimately connected to international developments, and along with the gradually increasing of the interest on documentary films, the discussions on art field by the publics and related works have become more common than before. The Media Art Center was opened in 2007 to meet the general public's increasing interest in documentary films. It provides the workshops for research and development in the field of documentaries, and organizes a series of events on exploring the aesthetics of Taiwanese documentary films to help extend the viewer's understanding of Taiwanese documentaries.