The necessary funding is the basic premise and important guarantee for the development of higher education. As the main source of funding for higher education, the amount of government fiscal input has a great affection on the development of higher education. Based on the study of fiscal funding input in higher education, this paper analyzes the present situation of fiscal funding input of higher education in Fujian province by means of statistical analysis and comparative study. It is found that there are some problems in fiscal funding input of higher education in Fujian, such as insufficient fiscal input, obvious regional differences and low expenditure efficiency. And on this basis, we put forward some corresponding suggestions, such as increasing the fiscal funding input in higher education, allocating the resources in higher education reasonably, and establishing the supervision system of fiscal input in higher education.