Objective:To analyze the correlation between the operational efficiency and comprehensive performance in primary medical institutions. Methods: Operational efficiency of 18 primary medical institutions at Jieshou in Anhui were assessed by Topsis method, and the correlation between the operational efficiency and comprehensive performance were explored by both parametric and nonparametric tests. Results: Operational efficiency of these 18 institutes was relatively low, and serious polarizations existed in the balance rate, debt to assets ratio, total assets turnover, inventory turnover, and etc. Results of performance evaluation were not related to the operational efficiency (P > 0.05). Conclusion: Performance-based financial compensati-on mechanism should strengthen the government financial investment responsibility and guide the institute managers to improve the operational efficiency.