With the help of data from Compilation of Statistics on Science and Technology of Colleges and Universities by the Ministry of Education, the paper analyzes the current situation and trend of input and output data of scientific research activities in China's medical colleges and universities from 2011 to 2017, and puts forward suggestions for the allocation of medical colleges and universities' input, including optimizing the structure of researchers, establishing scientific research performance incentive mechanism, broadening funding sources channels, etc.