The Agro- scientific Research Projects in Public Interest, a new national science and technology program proposed in the “Eleventh Five- Year”, has been an indispensable part of national science & technology innovation system since its implementation. From the aspects of its goal, organization manner, implementation and management, this paper summarizes the implementation experience of this kind of projects: highlighting public interest, entrusting the best, collaborating, perfecting system and building management platform. After analyzing the problems of single mode for collecting projects, insufficient function of science & technology department, lack of specific evaluation contents and procedures in the course of present operation system, it proposes some strategies on collecting projects widely to ensure the sources are more in line with actual production, stimulating the initiative and enthusiasm of the science and technology department of the research institutions, and designing the evaluation contents and indicators scientifically.