An airport is a complicated system that serves as a vital link in the aviation system. Airplanes are also a popular mode of transportation for daily travel and tourism. Now that COVID-19 is spreading over the world, many airlines are under severe financial strain. Therefore, long-term air traffic planning is critical, especially since the airport is a key region for COVID-19 to expand. To anticipate, simulate, and estimate the medical and health expenditures caused by the propagation of the epidemic under lax, mild, and strict social contact intervention, we utilize a hybrid model of the agent-based model and discrete event simulation. An agent-based model can capture individual behavior, and discrete event simulation can be used to explain the entire boarding process. Limiting the rate of wearing masks while traveling and upgrading airport facilities are the most effective strategies to manage the epidemic, given the convenience of travelers and the swift recovery of the national economy. Simulating passenger boarding will aid government agencies in improving airport equipment and facilities, facilitating passengers’ reasonable travel plans, avoiding large-scale contact, preventing the spread of epidemic diseases, and promoting the long-term sustainability of densely populated public transportation systems such as airports.