Based on the panel data of 12 prefectures and cities in Inner Mongolia from 2013 to 2023, this paper measures the spatio-temporal differences and dynamic evolution trends of the efficiency of medical and health care fiscal expenditure in Inner Mongolia using the three-stage DEA-Malmquist model, and analyzes the influencing factors of the efficiency values using the Tobit model. The research shows that the average comprehensive technical efficiency of medical and health care fiscal expenditure in Inner Mongolia is 0.814, and the insufficient scale efficiency is the main constraint factor. The regional efficiency shows a significant spatial heterogeneity feature of decreasing from east to west. The Malmquist index fluctuates from 2013 to 2023, with technological progress as the core driving factor. The urbanization rate and fiscal autonomy have a significant positive impact on the efficiency of medical and health care fiscal expenditure, while the education level, per capita disposable income, and fiscal burden rate have a significant negative impact on the efficiency. On this basis, suggestions for optimizing and improving the efficiency of medical and health care fiscal expenditure in Inner Mongolia are proposed, providing a reference for the optimal allocation of provincial medical and health care fiscal resources.