How to ensure the operating performance of farmer in the agricultural industrial production process is very important. This paper take the unique institutional innovation pattern of agricultural industrialization such as “company +cooperative+peasant household”as a example，and analyzes the motivation of why to Create the mode、 highlight of institutional innovation and operation performance. The results showed that the mode ensures the households' main position through institutional innovation in the agricultural industrial production process，and it is feasible to coordinate the interest conflict between the company and the peasant household through cooperative，and if the main position of cooperative can be really implemented that the effects of institutional innovation will be more good.