The main difference between rural and urban area inundation is the existence of an impermeable layer and the complexity of the road and building configuration. Therefore, although surface overland flow can be appropriately simulated by the two‐dimensional diffusive model in a rural area, there also is a need for a more accurate and elaborate simulation model. Dual drainage concept has been popular to simulate urban drainage system. Although the concept has immense advantages, through which overland flow and pipe flow can be simulated simultaneously, many researchers set manholes as discharge exchange spots between ground surface and sewerage system, which causes lack of reality. Therefore, in this study, we developed a new urban inundation model that can reflect real field situation. Also, two kinds of simulations are carried out with homogeneous meshes and non‐homogeneous ones using manholes and storm drains as discharge exchange spots, respectively, and those results are compared to estimate the effect of road networks and building groups according to different discharge exchange spots. Two‐dimensional run‐off flow model and one‐dimensional slot‐model are used to simulate ground surface run‐off flow and sewer pipe flow. To connect both models, we used a newly suggested bi‐directional model and its coefficients. The simulated results showed that more reasonable results are obtained in the nonhomogeneous case; the results further reveal the importance of using storm drains as exchange spots in the model.