Based on the panel data of 73 small and medium-sized airports in China from 2013 to 2021,the DEA (data envelopment analysis) model is used to calculate the airport operation efficiency, and the panel data is analyzed by regression analysis. The study found that the operational efficiency of domestic small and medium-sized airports showed an upward trend from 2013 to 2019, but from 2020 to 2021, due to the impact of COVID-19, the operational efficiency decreased significantly. Further research shows that airport subsidies have a significant positive effect on the operational efficiency of small and medium-sized airports. Although airport efficiency cannot directly affect subsidies, airport business volume has a positive and significant impact on subsidies. Therefore, some suggestions are put forward, including strengthening policy support for small and medium-sized airports, focusing on improving airport business volume, and establishing a mechanism to deal with emergencies, so as to promote the sustainable development of small and medium-sized airports.