Abstract:using DEA - HR - LCV three-stage method, measure and analysis of agricultural science and technology innovation system on the synergy innovation ability,the subsystems of mutual integration degree and restricting factors . Study conclusion shows that: (1) the scale efficiency is the main restriction factors of agricultural science and technology research and development team and farmers to improve technical efficiency, professional associations as a new type of agricultural science and technology popularization and socialized service organizations, its technical efficiency is significantly higher than traditional popularizing agricultural science and technology department; (2) Professional associations organized into a significant boost collaborative innovation ability of agricultural science and technology innovation system, the overall "coordination and general effective" status, but there are big room to improve, and agricultural technology innovation chain and industrial chain of "extremely weak convergence" is the main restriction factor ; (3) agricultural science and technology among the subsystems of the system is not yet implemented depth fusion, and there is a big regional differences, especially between agricultural technology innovation chain and industrial chain, presents the fusion "very weak" status, the reason is mainly insufficient research and development, insufficient agricultural technology promotion and socialized service and the lack of agricultural science and technology adopted and application. Based on the above research conclusion, the author put forward to speed up the new operators to cultivate and improve, deepening the reform of agricultural science and technology system, strengthening depth integration between agricultural technological innovation chain and industrial chain, as well as build and perfect the agricultural science and technology innovation system on the synergy mechanism of targeted countermeasures and Suggestions.