With global climate change and urbanization development, urban flooding occurs frequently and seriously affects urban development, so it is important to study the impact factors of waterlogging and carry out waterlogging risk assessment for disaster prevention and mitigation. Taking the main urban area of Beijing as the study area, we obtain the spatial data of waterlogging and the data of influencing factors, and use the MaxEnt model to explore, identify the potential risk area of waterlogging and analyze the relationship between influencing factors and the risk of waterlogging, and the results show that: (1) The dominant factors affecting the risk of flooding are distance from overpasses, building density, percentage of impervious surface, population density, storm duration, and NDVI; (2) More than 24.6% of the study area is at risk of flooding, with a total area of about 40.17 km2 in the high-risk zone and 298.09 km2 in the medium-risk zone; the lower-risk and low-risk zones cover 423.75 km2 and 30.53 km2, respectively; (3) the distribution of the number of flooding points in each district size relationship for Fengtai District > Haidian District > Chaoyang District > Shijingshan District > Xicheng District, Dongcheng District; historical flooding points in the spatial distribution of the distribution pattern of the "dense south and sparse north, dense west and sparse east," and "multi-core centers, sub-centers connected to the band" characteristics; (4) Spatial autocorrelation analysis of the risk assessment results found that the probability of risk in the middle of Fengtai District, the northeastern and southern part of Haidian District, and the eastern part of Shijingshan District is a high-high aggregation, indicating that the region may be affected by the surrounding areas and flooding disasters occur in the future, and that we should pay close attention to the region to achieve precise prevention and control. The results provide a certain reference for cities to carry out infrastructure improvement and renovation, prevention and control of potential flooding and waterlogging points, and the development of emergency mitigation plans and countermeasures.