Land suitability assessment is fundamental in space control planning and land development because of its effects on land use and urban layout. Rainstorms and waterlogging have become one of the most common natural disasters in the coastal areas of China. As a result, the concept of an ecological sponge city was incorporated into the construction of cities in the future. Taking Shenzhen–Shantou special cooperation zone (SSCZ), we constructed a storm flooding model based on the SCS flow generation model and GIS to explore the spatial distribution characteristics of the flooding risk in a rainstorm of 100-year lasting 1 h. Combined with population and economic indicators, a radial basis function (RBF) network was utilized to evaluate the environmental risk, the vulnerability of disaster-bearing bodies, and the rain–flood resilience of sponge cities. The self-organizing feature mapping (SOFM) model was used for cluster analysis. Spatial differences were found in the construction suitability of the study area. A suitable construction area (73.59% of the entire area) was located downtown. The construction of the artificial spongy body in the highest vulnerable area (3.25%) needs to be strengthened. The control construction area (3.3%) is located along the banks of the river, with relatively high risk and low resilience of flood control engineering. Ecological construction (19.85%) serves as the sponge body of ecological buffer. The factors of waterlogging, ecology, population, and economy could be integrated comprehensively by applying neural network methods for urban planning and construction.