This paper analyzes the institutional evolution process of farmer cooperative economic organization since the founding of new China. The institutional evolution logic is dominated from regulative factor, to normative factor, to cultural-cognitive factor. The results show that the single institutional factor would lead to the problems of organizational change, the lack of organizational development motivation and the lack of normative. Therefore, this paper presents recommendations about continued perfection of legal system, adjustment of policy supply direction and shaping of cooperative values from the coordinated development level of three factors.