In 1985,Issued by the State Education Commission《Notice on carrying out evaluation research and pilot work of Higher Engineering Education》, Some provinces and cities first started the pilot evaluation of running colleges and universities, By early 2012, Issued by the Ministry of Education《Measures for the implementation of qualification assessment of undergraduate teaching in ordinary colleges and Universities》and 《Evaluation index system of undergraduate teaching qualification in Colleges and Universities》, After years of unremitting exploration, the undergraduate evaluation system of colleges and universities has been gradually improved and perfected. China has basically determined to integrate the school running idea, teaching staff, teaching conditions and utilization. However, with the development of society and the continuous improvement of people's demand for education, there are unavoidable problems in the evaluation system of colleges and universities, From the perspective of new institutional economics, this paper attempts to put forward some suggestions on how to promote its development in order to better serve the cause of higher education.