The article mainly discusses how to evaluate research quality of universities and colleges in Taiwan. At frist, it refers to the Research Assessment Exercises in the UK which provides ratings of the quality of research conducted in universities and colleges in the UK, to inform the selective allocation of funds in accordance with the quality of the work undertaken. The expert peer review system which is the evaluation mechanism of RAE is explored with evaluation procedures in the study. Citation analysis with its application is also studied in the article. As citation analysis is bibliometrics and it is not suitable for applied as a main tool in research assessment of universities and colleges. At last, the article makes some conclusions that it is necessary to develop the research assessment of universities and college in Taiwan with expert peer review, besides, SCI, SSCI and citation counting data can be used as a metric information for reference.