Using the method of structural equation and balanced scorecard, this paper establishes the evaluation indicators and evaluation model for the performance of 21 rural cooperative economic organizations in X City of Hunan Province, and analyzes the relationship between indicators and dimensions of performance evaluation indicators, in order to find the influencing factors, obstacles and successful experience concerning the development of rural cooperative economic organizations. According to model analysis and conclusions, this paper sets forth the recommendations for promoting the development of rural cooperative economic organizations in Hunan Province, in order to provide a scientific basis for the institutional design and mechanism innovation of rural cooperative economic organizations in Hunan Province.