Abstract: The innovation capability of agricultural scientific research institutions will directly determine the progress of agricultural science and technology and the development way of modern agriculture. To objectively and comprehensively evaluate the innovation capability of agricultural scientific research institutions, the innovation process was analyzed, the innovation factors were explicated and an evaluation index system was built up in light of scientific theories on system and management. AHP and comprehensive evaluation method were combined to set up the fuzzy synthetic evaluation model which was applied to the national-level agricultural scientific research institutions. According to the results, the institutions were divided into four types which were scientific and technological innovation style, scientific innovation style, technological innovation style, and fundamental ability style. This classification method can not only adjust the direction and strength of science and technology system reform, but also implement classified guidance and management.