Abstract: By combining the current achievements in research and the development practice of rural mutual fund organizations，the paper built a risk model on uncertainty of the external environment and adjustment of internal organization. Based on this model，the paper built the risk identification system of rural mutual fund organizations. With 36 rural mutual fund organizations in Yancheng，Jiangsu，the paper used questionnaires and the method of factor analysis to identify the key risk types and followed in the order of importance：decision supervise risk，managers risk， competition risk，incentive risk，external regulatory risk，financial risk，size risk，policy and economic risks. Building sound internal governance mechanism to restrict the internal control，regulating the rural financial market environment and improving the regulatory policy may help reduce the key risks.