Airport runway drainage is one of the key factors in ensuring the safety of aircraft operation and aircraft quality, and a good drainage system can effectively remove rainwater and reduce the impact of stagnant and retained water. To explore the drainage capacity of the existing airport runway drainage system, as well as the evolution process of rainfall and drainage system, an airport-runway in southern China was taken as the research object, applied the Danish Hydraulic Institute model integrated computing(DHI MIKE) model to the airport runway, and the coupled rainfall and flooding model was constructed. According to the rainfall characteristics of the study area and the existing drainage system, four rainfall scenarios with different recurrence periods were designed, and simulation analyses were conducted from three aspects: pipe fullness, surface inundation results, and runway waterlogging evolution process. The results show that the number of full pipes is positively related to the rainfall intensity, and the spatial distribution of water depth in the study area under different recurrence periods is generally consistent, concentrates around the shallow catchment ditch. The larger the recurrence period, the higher the water depth. The time of water accumulation and runway closure are advanced. The runway drainage capacity can meet the standard of one in five years of rainfall.