Abstract：Objective: Analyzing the efficiency of medical system in China and examining the impact of the imbalance of regional health system efficiency on the health status of residents. Methods: Using DEA method to measure the output efficiency of inter - provincial medical system in China; Employing the panel quantile regression model to measure the health improvement effect and changing trend brought by the promotion of the efficiency of medical system. Results: The efficiency of health systems in different provinces in China shows the situation of high in the east and low in the west, regional imbalances are obvious; the impact of the promotion of efficiency of the medical system on the residents’’ health status will be weakened with improvement of residents’’ health status. In areas where the residents’’ health status is the best, the effect of improving the efficiency of medical treatment has been no significant. Conclusion: We should give full play to improvement effect of medical system efficiency on the residents’ health, focusing on supporting the construction of medical systems in backward areas to promote the balanced development of China’’s regional medical system.