As an important transportation hub for air transportation, airports have played an important role in promoting regional economic and social development and improving the comprehensive national transportation system. The exploration of the key factors affecting the airport’s operational capacity are of great importance to the sustainable development of the civil aviation transportation industry. In order to investigate the effect of airport operation, this paper selects 13 major airports in China’s three major airport groups as the objects, defines the airport operational capacity by using entropy method combined with relevant indicators, calculates and sorts the operational capacity of sample airports, and analyzes the operational capacity of their internal airports by taking airport groups as units. By using the Tobit regression model, this paper analyzes the important factors that affect the operational capacity of sub-airports within the airport group. The results show that the economic level, urban development and the degree of opening to the outside world have a positive impact on the airport operational capacity. Different regional airport groups have different influencing factors on internal sub-airports’ operational capacity.