Flood/waterlogging risk analysis was conducted of the inland side of the Shenzhen River Basin based on key factors, including disasters inducing factors, disaster-pregnant environment, disaster-bearing body, and the capacity of disaster prevention and reduction. A flood/waterlogging risk evaluation index system of coastal cities was established, which was characterized by hazard risk resulted from the complex risk inducing factors with superposition of rain, flood, and tide as well as high vulnerability risk caused by high urbanization. The entropy weight was modified with the analytic hierarchy process to carry out the weight distribution of indicators, and the flood/waterlogging hazard risk, vulnerability risk, and comprehensive flood risk zoning were obtained. The results show that the southwest of Futian District to the southwest of Luohu District was identified to be a unity with extremely high risk of hazard and vulnerability, which deserves to be prioritized in flood/waterlogging prevention and mitigation in all aspects, while the low-vulnerability but high-hazard area should be given customized protection measures based on the leading risk factors. The flood/waterlogging risk evaluation index system of coastal cities can provide a necessary reference for government in disaster prevention and mitigation planning and emergency response, and it can also provide effective information for disaster prevention resources allocation and post-disaster reconstruction.