This work aims to effectively resolve the problem of waterlogging in cities and manage water resources in sustainable cities. Digital Twins (DTs) technology was applied to the Urban Drainage System (UDS) and solves the modeling and scheduling problems of emergency drainage through the core model construction method of DTs. Firstly, the components of the UDS that are necessary in the process of building the model were listed according to the entity elements of the five-dimensional (5D) DTs model. Then, this work analyzed the essential data of the DTs of UDS and the Data Collection method according to the data elements of the 5D DTs model. Finally, the Multi-Level Dynamic Priority and Importance Scheduling (MDPIS) algorithm was proposed based on the Fixed Priority Scheduling (FPS) algorithm, which was verified by the simulation experiment. The experimental results indicated that the MDPIS algorithm showed significant performance in the rainfall scene with large fluctuations compared with the FPS algorithm. Specifically, the average improvement ratio was the highest, reaching 49.81%; the overall improvement rate was constant at about 48%. The operation results showed an apparent correlation between the catchment parameters and the overflow loss of the pumping station. The improved MDPIS algorithm can effectively utilize the water storage capacity and drainage capacity of the pumping station and reduce overflow losses during rainfall by dynamically adjusting the priority to solve the problem of urban inland inundation. The DTs-based UDS proposed here can effectively mitigate the overflow loss and improve the working efficiency of the pumping station cluster, promoting the development of Substainable Cities.