It is a common phenomenon in cities that waterlogging affects people’s normal life. It is of great significance for targeted transformation and upgrading to identify the risk factors of urban waterlogging. This paper collected the waterlogging data of Tianjin in China, analyzed the coupling mechanism among waterlogging risk factors of urban drainage systems, and then selected the system dynamics theory and the Vensim software as the analysis tools due to the mixing characteristic and the limited availability of data. After that, the sensitive factors were identified by model simulation and sensitivity analysis, and the prominent impact of urban expansion on waterlogging risk was discussed. Then, through the comparison of the three simulation scenarios, it was found that, compared with the urban development focus shifting strategy, the strategies of sponge city reconstruction and management optimization could achieve the risk control goal within a shorter time. On this basis, two kinds of governance schemes with strong operability were put forward, which were the data governance strategy and the sponge city reconstruction strategy of giving priority to old urban areas. According to the simulation results, a city can reverse the increasing trend of waterlogging risk within ten years under the appropriate scheme. Furthermore, the paper puts forward the strategic reimagining of the rural revitalization strategy and the ecological restoration strategy for the long-term sustainable development transformation of Tianjin.