Based on the relevant action subject in the cooperative governance structure,this paper analyzes two cooperative governance structure modes,namely “General Assemblythe Council” and “Ordinary members-Core members-the Council” with the field survey data and case study in the framework of principalagent theory. Specifically,this paper analyzes operation process and governance situation of two modes by using the case from apple growers’ cooperatives. The result shows that compared with the governance structure mode of “Ordinary membersCore membersthe Council”,members of “General Assemblythe Council” mode are more likely to participate in the governance of cooperative. Meanwhile,the mode of “General Assemblythe Council” has the advantage of saving management transaction cost and market transaction cost. The reasons for this include three aspects which are different in the motives of the members based on the two governance structures,the different demands of interests,the different logical framework of the principalagent relationship,the existence of significant information asymmetry among members,as well as the difference of market transaction cost. Therefore,this paper proposes several countermeasures on how to optimize the governance structure so as to provide theoratical base for the governments to make policy to promote the deveopment of cooperatives.