Abstract: In this paper, combined with the development practice of modern character agriculture in Fujian Province, key development direction of agricultural science and technology innovation were briefly stated based on survey of agricultural scientific research institution development and formulation of development plan. Aiming at great and key technical problems in the fields of food safety, green development, pollution regulation and facility agricultures, which holdback the development of modern agriculture with special characteristics in Fujian Province, some ideas of eight key agricultural science and technology research projects were discussed. Countermeasures were also proposed to deepen coordinated innovation and cooperative research. Meanwhile, opportunities and challenges facing deepening reform of agricultural scientific research institutions were analyzed and some suggestions were put forth to further implement innovation of management mechanism.