Based on the elaboration of the content and status of rural cooperative finance, rural cooperative finance——the alienation of rural credit cooperative is introduced from three aspects of the concept and objective of management, the organizational form and management mode, and the service object and business scope. Causes of alienation are analyzed. Firstly, change in the economic foundation of cooperative finance is the fundamental reasons for the alienation. Secondly, mandatory system change led by the government is an important reason for alienation. Thirdly, property and administration structure of rural credit cooperative are the internal reasons for alienation of agricultural support. To achieve the innovation of rural cooperative financial organization, the following aspects should be done: cultivating the basis for rural cooperative economy, further promoting the reform of rural credit cooperatives (innovating a variety of property rights modes; making clear definition of ownership; implementing the internal governance structure), introducing competition in the field of rural cooperative finance, and homing function of government and rural cooperative finance.