In order to better integrate research resources of National Central University, National Chiao Tung University, National Tsing Hua University, and National Yang-Ming University, UST has organized several research centers to pursuit academic excellence. Considering the research strength of the four universities and after rigorous planning and review process, Brain Research Center and Center for Nano Science and Technology have been inaugurated in 2003, and Center for Advanced Information Systems and Electronics Research and Center for Environmental and Energy Research, have been established in 2004.

Each research center has research as well as education programs jointly participated by faculties from the four universities. The administrative structure of each research center is as follows:

The Director of a research center is nominated by the UST Chancellor and approved by the UST Steering Committee. The Steering Committee of each research center, its members appointed by the UST Chancellor, provides guidance in research direction of the center. The Advisory Committee of each research center, its members also appointed by the UST Chancellor, gives technical advices on the formation of each research project within the center and is responsible for reviewing the performance of the center.