To further investigate the impact of the COVID-19 pandemic on the operational efficiency of hospitals in China, this article uses the DEA-Malmquist model to measure and analyze the operational efficiency of hospitals in 31 provinces across the country from 2015 to 2021. The research results indicate that environmental factors have reduced the operational efficiency of hospitals to some extent. In terms of the regional characteristics of efficiency, the mean total factor productivity in the southern regions is higher than that in the northern regions, but the average annual growth rates of comprehensive technical efficiency, pure technical efficiency, and scale efficiency in the northern regions are higher than those in the southern regions. In addition, the COVID-19 pandemic has had a significant impact on the operational efficiency of hospitals. The total factor productivity of hospitals in 2020 decreased by 19.6% compared to the previous year, and the comprehensive technical efficiency of hospitals in the northern regions decreased by 2.3% during the same period, while the southern regions showed an increase of 0.6%. The northern regions are more vulnerable to the impact of the pandemic.