Taking Environment and Plant Protection Institute in Chinese Academy of Tropical Agricultural Sciences as an example, it summarized major experience and practice in management of scientific research projects from strengthening project database, enhancing project planning, reinforcing scientific research management team construction, bringing into play functions of academies and institutes, and improving management system. It analyzed existing problems and came up with recommendations from strengthening project process management, improving management team quality, and improving incentive mechanism, in the hope of providing reference for scientific research project management in agricultural scientific research institutes.