New institutional economics regards the effective organization form as one of the extremely important social resources in social economic development. The important meaning of the rural cooperation system lies in the forming of cooperation among scattered peasants through official or unofficial organizations and realizing community self-management of certain areas on the base of the recognition of community's interests and common norms. This article attempts to analyze the reasons from institutional economics angle why new type rural cooperation system is hard to set up, and to find out the impact of economic system, political system and cultural customs on the development of rural cooperation system.