Based on the previous research, a total of 10 risk indices are selected according to the specific situation in Sichuan Province, such as natural risk, resource constraint risk, internal management risk, capital risk, technical input and output risk, market risk, contract credit risk, property risk and policy support risk. According to the questionnaire survey by cooperative economic organization of Sichuan Province, principal component analysis is used to analyze the importance and influence degree of the operation risk of rural cooperative economic organization. Result shows that in the operation of cooperative economic organization, management risk has greater influence degree and importance degree, which should be paid special attention to. Capital, property, price fluctuation, and quality of members have great degree of risk and are paid little attention to. The technical input and output risk and the contract credit risk have relatively low impact on the operation risk of cooperative economic organization and their importance is relatively low. Therefore, we should continue to maintain its advantages. Nature, resource constraint and policy support have relatively high risk awareness and low influence degree, belonging to the factors with priority attention which are controlled to some extent. Finally, suggestions are put forward, such as enhancing the management level of cooperative economic organizations, strengthening the farmers’ risk awareness, and improving the risk aversion ability of cooperative economic organization.