The agricultural scientific research project funding is an important prerequisite for the implementation of agricultural scientific research project, and an essential basic condition to support agricultural research. In recent years, China has paid great attention to the development of scientific research, and increased the input of scientific research funds, but there are some shortcomings in funding management during the implementation of the project. Based on many years of practice, this paper expounds the main problems in the current funding management for agricultural scientific research project, and brings forward the relevant recommendations, in order to provide a reference for the scientific management of agricultural scientific research project funding in the new situation.