In 2016, 192 cities, including Wuhan, Nanjing, and Jiujiang, suffered from severe flooding, which raised social and government concerns in China. This paper proposes a method based on the underlying surface to estimate the urban flood-carrying capacity. First, water is extended into the underlying surface vegetation-impervious surface-soil (VIS) model to form the vegetation-impervious surface-soil and water (VIS-W) model. Second, the watershed is delimitated using a digital elevation model (DEM). Third, the natural water system’s storage capacity, including rivers, lakes, and puddles, is estimated. Using the rainfall–runoff hydrology model and the VIS-W model, the storing ability, the receiving ability, the discharge potential, and the emergency of pumping outward are assessed to derive the final flood-carrying capacity. Finally, the result is compared with data on the waterlogging points collected in July 2016 during a flood and waterlogging event in Wuhan. It is found that 84% of waterlogging points are located in the “weak” or “normal” areas, and 16% are located in the “strong” areas. Additionally, 99% of total waterlogging points are located upstream, based on the stream extracted by the DEM. This phenomenon indicates that Wuhan can mitigate flood disasters by fully utilizing the natural water system storage capacity to corporate the city’s drainage schedule.