Abstract: Using DEA method, this paper empirically studied the relationship between input and output efficiency of protecting farmers’ homestead rights and interests in the pilot reform process of rural homestead system in Dali city. On the basis of calculating the efficiency value, tobit regression model was used to analyze the key factors affecting the efficiency of protecting farmers’ homestead rights and interests, so as to seek an effective path to improve its efficiency. It was found that the efficiency of protecting the rights and interests of farmers’ homestead was positively correlated with the development of non-agricultural economy; The significant factors affecting the protection efficiency of farmers’ homestead rights and interests in Dali were the average household population, the compensation standard for land acquisition, the per capita land area of rural settlements, and the rate of confirmation and certification of homestead. In this regard, this study proposed that we have to combine the “separation of three rights” reform of rural homestead, adhere to the “one household, one house” and the guidance of village planning, fully expand the usufruct of homestead, realize the extension of the function of means of living to the function of means of production, and make deepening the reform of rural homestead system become an important engine to promote the integration of urban and rural development and increase farmers’ property income.