Objective: By comparing and analyzing the operational efficiency of 18 tertiary public hospitals in Heilongjiang province, references and suggestions are provided for optimizing operational efficiency in the context of the current “national examination”. Methods: An input-output operational efficiency evaluation index system is constructed based on the national performance appraisal manual. DEA-Malmquist index method is applied for dynamic and static analysis. Results: The average comprehensive technical efficiency value is 0.963, 12 out of 18 public hospitals have effective operational efficiency DEA, and the average total factor productivity is 1.174, the overall level is high and overall positive; the extreme difference of comprehensive technical efficiency in the sample in 2021 is 0.211, and the extreme difference of total factor productivity is 0.260, and the development difference between hospitals is obvious. Conclusion: The overall operational efficiency of the three-tier public hospitals in Heilongjiang Province turned to be well after the decline of epidemics, but the province’s technical progress index fluctuates greatly, warning hospitals to realize the scientific management process needs to be prepared well. Meanwhile, it needs to focus on human, material and financial resources, give full play to the scale efficiency brought about by the comprehensive technical efficiency, in addition to the tertiary public hospitals between the development of the problem of imbalance is still more prominent, the need to improve from the allocation of resources, operational structure, management level and investment scale, to further enhance the operational efficiency of hospitals, improve the performance appraisal system.