Based on panel data of 12 prefecture-level cities in Inner Mongolia from 2013 to 2023, this paper measures the spatiotemporal variations and dynamic evolution trends of healthcare fiscal expenditure efficiency in Inner Mongolia using the three-stage DEA-Malmquist model, while analyzing the influencing factors of the efficiency values using the Tobit model. The result shows that the average comprehensive technical efficiency of healthcare fiscal expenditure in Inner Mongolia is 0.814, with insufficient scale efficiency identified as the main constraint. Regional efficiency shows significant spatial heterogeneity with a decreasing pattern from east to west. The Malmquist index exhibited a fluctuating trend from 2013 to 2023, with technological progress as the primary driving factor. The urbanization rate and fiscal autonomy have significant positive impacts on the efficiency of healthcare fiscal expenditure, while the education level, per capita disposable income, and the fiscal burden rate have significant negative impacts on the efficiency. Research indicates that it is necessary to enhance the efficiency of healthcare fiscal expenditure in Inner Mongolia by establishing a comprehensive fiscal budget management system, developing regional dynamic monitoring and precise management, clarifying expenditure responsibilities, optimizing fiscal decentralization, strengthening preventive priority investment, and promoting technological innovation.