The acquisition of high-resolution digital elevation model (DEM) data is an on-going challenge in urban flood modeling, especially for larger domains. The accuracy of flood simulations is significantly dependent on the precision of DEM data. To address this issue, we propose a method of modifying mid-resolution DEM data to provide a realistic ground elevation for urban flood modeling using geographic information system (GIS) tools. The modified DEM contains the properties of the existing digital terrain and digital surface model (DTM and DSM) data. Flood calculations were performed using 2D shallow water and kinematic equations in the integrated multiscale simulation scheme developed in recent literature and tested for an extreme flood event in an urbanized area in the Philippines. The results show that the underestimated and overestimated flood tendencies for DTM and DSM, respectively, were adequately resolved in MDEM simulations, which were able to accurately capture the flood propagation along the natural and artificial barriers in the urban area, as compared to untreated DTM and DSM data, with root mean square error (RMSE) improvements from RMSEDTM = 30.64 and RMSEDSM = 17.28 to RMSEMDEM = 0.17. The proposed method significantly improved the accuracy of the simulations. It would allow high-resolution urban flood modeling with limited detailed elevation data, which is crucial to propose adequate flood action plans specifically for developing countries experiencing frequent rainfall events.