Abstract Made an empirical study on the relationship between the college scientific research fund input and the research process in China by using the fixed effect model and the data of natural science research fund input of the universities in China from 1997 to 2015, thus confirming the experience knowledge and development logic of the investment and research process of scientific research. The research results show that the source structure of the scientific research fund input in our country is still vertical research funds supported mainly by the government, and the vertical research funds play a significant role in the development of the scientific research process. The horizontal research funds supported by the society play a quite important role, which need to be improved. The efficiency of scientific research fund input in Universities of China needs to be improved. The researchrelated fees in university have a positive effect, but its contribution is unsatisfactory. The investment of per capita service fee has not promoted the development of college scientific research a lot in our country. The reform of China's scientific research fund in colleges is effective, and the investment of the researchrelated fees tends to be rationalized. The negative effect of the development of scientific research caused by the service fee input, has been weakened.