With the rapid development of higher education in our country, China is increasing its financial investment in colleges and universities, and the amount of funds for fiscal expenditure projects in colleges and universities is increasing. The performance evaluation of the fiscal expenditure project is an important management way and effective means to ensure the rational use of these special funds and optimize the allocation of the funds. This paper elaborates the necessity of performance evaluation of fiscal expenditure project in colleges and universities in China. On the basis of analyzing the present situation of performance evaluation of fiscal expenditure project in colleges and universities in China, this paper puts forward some suggestions and improvement measures to optimize the performance evaluation index system of university fiscal expenditure.