With the acceleration of the urbanization process, waterlogging problems in coastal cities are becoming more and more serious due to climate change. However, up until now, the common procedures and programs for rainstorm waterlogging risk assessment in coastal cities still have not formed. Considering a series of impact factors of rainstorm waterlogging in coastal city, the present study established a paradigm for rainstorm waterlogging risk assessment through the combination of hydrological modeling and GIS spatial analysis, and took the residence in central urban area of Shanghai as an example. First, the simplified urban waterlogging model was applied to simulate the depth and extent of rainstorm waterlogging under six hypothetic scenarios. Second, the residence exposed to rainstorm waterlogging was extracted and analyzed supported by spatial analysis module of ArcGIS. Then, stage-damage curves were applied to analyze the loss rate of structure and contents of residential building. Finally, the waterlogging loss maps of residence in different scenarios, the annual average loss, and the risk curve were taken as the expression of waterlogging risk. The results show that the inundated water depth, vulnerability, and losses of residence all increase as the intensity of rainstorm increases. The old-style residence is most vulnerable to rainstorm waterlogging, followed by the new-style residence, and villa is less vulnerable to rainstorm waterlogging. The annual average loss of residence in Shanghai central urban area was about CNY 22.25 million. The results also indicate high risk in Yangpu and Putuo districts, Xuhui, Hongkou, Changning and Zhabei districts come under medium-risk zone, and Jing’an, Luwan and Huangpu districts come under low-risk zone. These results provide important information for the local government, and the methodology can be applied in other cities to provide guidance on waterlogging risk governance.