Abstract: The research used the method of unified structural equation of balance scorecard to establish the farmer cooperative economic organization performance evaluation index and evaluation model. The evaluation index and model were applied to the evaluation of 21 farmers' professional organization performance in X Hunan City, for analyzing the relationship between the index and the index of performance evaluation of each dimension. The author tried to find factors, obstacles and successful experience that influencing the formation and development of the farmer cooperative economy organization. Based on model analysis, the author put forward relevant suggestions to promote the farmer specialized cooperative economic organization in Hunan province and provide scientific basis for farmer cooperatives’system construction and mechanism innovation.