Project management of agricultural scientific research institutions is an important section of agricultural scientific research plan management. It is of great significance for sustainable development of scientific research work of scientific research institutions. According to a series of opinions and notices about scientific and technological system reform issued by the state, and combining current situations of management of scientific research projects in scientific research institutions, this paper made a preliminary study on management of agricultural scientific research projects in the new trend. Finally, on the basis of the current situations of management of agricultural scientific research projects, it came up with pertinent recommendations, including strengthening communication and cooperation and actively declaring projects, strengthening preliminary planning of projects and establishing project information database, reinforcing project process management, ensuring on-time and high quality completion of projects, and strengthening learning and improving quality of management personnel.