Urban waterlogging is a natural disaster that occurs in developed cities globally and has inevitably become severe due to urbanization, densification, and climate change. The digital elevation model (DEM) is an important component of urban waterlogging risk prediction. However, previous studies generally focused on optimizing hydrological models, and there is a potential improvement in DEM by fusing remote sensing data and hydrological data. To improve the DEM accuracy of urban roads and densely built-up areas, a multisource data fusion approach (MDF-UNet) was proposed. Firstly, Fuzhou city was taken as an example, and the satellite remote sensing images, drainage network, land use, and DEM data of the study area were collected. Secondly, the U-Net model was used to identify buildings using remote sensing images. Subsequently, a multisource data fusion (MDF) method was adopted to reconstruct DEM by fusing the buildings identification results, land use, and drainage network data. Then, a coupled one-dimensional (1D) conduit drainage and two-dimensional (2D) hydrodynamic model was constructed and validated. Finally, the simulation results of the MDF-UNet approach were compared with the raw DEM data, inverse distance weighting (IDW), and MDF. The results indicated that the proposed approach greatly improved the simulation accuracy of waterlogging points by 29%, 53%, and 12% compared with the raw DEM, IDW, and MDF. Moreover, the MDF-UNet method had the smallest median value error of 0.08 m in the inundation depth simulation. The proposed method demonstrates that the credibility of the waterlogging model and simulation accuracy in roads and densely built-up areas is significantly improved, providing a reliable basis for urban waterlogging prevention and management.