In order to deal with the urban waterlogging disasters, a high precision three-dimensional (3D) Digital Elevation Model (DEM) is built in this paper. This DEM is based on high-precision data of urban topography and geomorphology, covering 3D surface elevation, road network and structures. The simulation calculation of this model can get different watershed area according to different elevation based on the topographic feature. Furthermore, divide the urban regional model into the stage sub-catchment area corresponding to the elevation. Within the sub-catchment area, it can also reflect the situation of urban waterlogging, in combination with the rainstorm intensity formula, the statistics of local area underlying surface, and Soil Conservation Service (SCS) model of runoff simulation. It can also help to simulate the submergence depth and range under different recurrence stages of rainfall scenarios. The research shows that this DEM model can provide the premise for the highly accurate numerical simulation of surface runoff and confluence, which can effectively improve the accuracy of the division of catchment area and the assessment, prediction of waterlogging disaster. This provides an important idea and method for the flood prevention and control in flood season for reservoir, tailings pond and urban waterlogging.