Whether the national agricultural policy can be effectively transformed into the implementation efficiency is an important measure of whether the state autonomy goal can be achieved in the grass-roots governance field. System, power and actors constitute an analytical framework for the state autonomy practice in the context of grass-roots governance. Through comparative analysis of multiple cases, it is found that the joint role of system, power and actor is the direct reason for the different performance of national agricultural policies implementation, which is closely related to the impact of local state autonomy and rural society autonomy on state autonomy. In different policy practices, the different relations between state autonomy, local state autonomy and rural social autonomy constitute the internal logic of the different state autonomy. The game practice of state autonomy shows that the state autonomy in governance practice presents a fragmented pattern, specifically manifested as the coexistence of dynamic and limited, hierarchical and mutual, which is the fundamental reason for the difference performance of national agricultural policies implementation. It is an important approach to improve the agricultural policy implementation efficiency to promote the universal formation of embedded and appropriate state autonomy through the system, power and actor.