Literatures about the institutional arrangement of the Peasant Special Cooperative Organization are summarized. Based on the introduction of theoretical background, the overall level of annual earnings in the year 2008 is selected as a dependent variable to evaluate the economic performance of cooperative organizations, according to the investigation on 54 Peasant Special Cooperative Organizations in Cuiping District, Sichuan Province, China. A total of 13 institutional indices passing the correlation test are chosen as independent variables. Relationship between the development level and the institutional factors affecting the economic performance of cooperative organizations is studied by using factor analysis method. Result shows that there is relatively high consistency between the score of institutional factor and the development level of cooperative organization. Both macroscopic support system and internal benefit distribution system have greater impacts on the Peasant Special Cooperative Organization; the internal supervision factor and the interest factor of core members have insignificant impacts on the economic performance; and the production management factor has little effect on economic performance. Based on this, several suggestions are put forward, including standardizing and reforming the system, improving the countermeasures for economic performance, strengthening the support and policy guidance for Peasant Special Cooperative Organization, improving and standardizing the distribution of benefit system, the security system and monitoring system for core members’ interests, and fully reflecting the interests of core members.