Objective: To analyze and compare the differences between the operation efficiency of hospitals in China during the "12th Five-Year Plan" period and the "13th Five-Year Plan" period, and provide scientific basis for improving the operation efficiency of hospitals. Methods: It describes the development level of input-output indicators of Chinese hospitals during the "12th Five-Year Plan" and "13th Five-Year Plan" period, and uses the DEA-Malmquist index model to analyze the operational efficiency of hospitals. Results: During the "12th Five-Year Plan" period, the operation efficiency of hospitals in China showed an increasing trend. Among 31 provinces (districts and cities), only the operation efficiency of hospitals in Tianjin, Inner Mongolia, Gansu, Ningxia, Tibet, Fujian, Hainan and Yunnan showed a downward trend, and the operation efficiency of hospitals in the other 23 provinces (districts and cities) showed an increasing trend. During the "13th Five-Year Plan" period, the overall operation efficiency of hospitals in China and the operation efficiency of hospitals in various provinces showed a downward trend. Conclusion: The reform and technical level of public hospitals may be the reasons affecting the operation efficiency of hospitals. The government should effectively control the scale of hospitals, improve the efficiency of resource allocation and utilization, and break down technical access barriers. Hospitals should improve their technical level and management ability.