Compared with other cities, the population density, GDP density and urbanization level of megacities are higher, and the life and property losses caused by urban flooding/waterlogging disasters are more serious. A scientific, systematic and comprehensive analysis of the causes of flooding/waterlogging disasters in megacities under the changing environment is critical for improving the urban flooding/waterlogging mitigation and disaster reduction system and reducing the losses caused by urban flooding/waterlogging disasters. Taking three typical megacities, including Beijing, Jinan and Shenzhen as examples, the characteristics of flooding/waterlogging disasters in these megacities were expounded, and the impacts of natural factors and anthropogenic factors on urban flooding/waterlogging were analyzed. The natural factors includes climate conditions, geographical conditions and precipitation changes, while the anthropogenic factors include runoff generation and concentration changes, stormwater regulation and storage capacity changes, drainage patterns and urban planning. The countermeasures for flooding/waterlogging disasters in megacities were proposed from three aspects, including deepening theoretical research, constructing forecasting platform and promoting the coordination of engineering and non-engineering measures, which can provide a scientific basis for the prevention and control of flooding/waterlogging disasters in megacities of China under changing environment.