Background: Over the last decade, the expenditure on public medical and health has increased greatly in China, however, problems as low efficiency and unfairness still exist. How to accurately describe the effectiveness of existing medical and health resources in combination with regional heterogeneity is of great significance to China's medical and health reform. Methods: Based on provincial panel data for the period of 2005 to 2017, combining expected output and unexpected output, this paper constructs a super-efficiency three-stage SBM-DEA model, to measure and analyze the spatial-temporal heterogeneity characteristics and influencing factors of public medical and health efficiency (PMHE). Results: (1) After the impacts of random error and external environmental factors are removed, the mean value of overall PMHE is 0.9274, failing to reach DEA efficiency, and PMHE shows a fluctuated downward trend. (2) The adjusted PMHE level shows a prominent spatial imbalance at the stage 3. The average efficiency level is ranked by the East > the West > the Central > the Northeast. (3) The increases of GDP per capita and population density are beneficial to the improvement of PMHE, while income level and education level are disadvantageous to PMHE, and last, the urbanization level, an uncertain effect. (4) There is no σ convergence of the PMHE in the East, the Central and the West, that is, the internal differences may gradually expand in the future, while the Northeast shows a significant σ convergence trending of PMHE. (5) The state's allocation of medical and health resources has undergone major changes during "The Twelfth Five-Year Plan". Conclusion: This study innovatively incorporates undesired outputs of health care into the efficiency evaluation framework by constructing the main efficiency evaluation indicators. The results of the robust evaluation conclude that China's existing investment in medical and health resources is generally not effective. Therefore, although China's health care reform has made certain achievement, it is still necessary to expand the investment in health care resources.