Abstract:With the release of a series of documents, the government departments actively promoted the management and use of financial research funds through simple administration and decentralization. Further stimulate innovation and create vitality. As one of the important subjects of building an innovative country, how to combine the actual situation, sum up the past experience, consider the future needs, and avoid the emergence of “Confusion and Stagnation” in the process of scientific research fund management reform. This is another major test of the ability of university. To this end, this paper will try to analyze the evolutionary game between the government finance department and university from the perspective of the budget management of financial research projects in the context of“streamlining administration, delegating more powers, improring regulation and optimizing services”, in order to create a benign interactive environment and effectively reduce the whole society. Regulate costs, improve the use efficiency of research funding, promote the reform of science and technology system, and promote the development of national science and technology innovation.