Urban flooding as a result of inadequate drainage capacity, failure of flood defenses, etc. is usually featured with highly transient hydrodynamics. Reliable and efficient prediction and forecasting of these urban flash floods is still a great technical challenge. Meanwhile, in urban environments, the flooding hydrodynamics and process may be influenced by flow regulation and flood protection hydraulic infrastructure systems, such as sluice gates, which should be effectively taken into account in an urban flood model. However, direct simulation of hydraulic structures is not a current practice in 2D urban flood modeling. This work aims to develop a robust numerical approach to directly simulate the effects of gate structures in a 2D high-resolution urban flood model. A new modeling component is developed and fully coupled to a finite volume Godunov-type shock-capturing shallow water model, to directly simulate the highly transient flood waves through hydraulic structures. Different coupling approaches, i.e., flux term coupling and source term coupling, are implemented and compared. A numerical experiment conducted for an analytical dam-break test indicates that the flux term coupling approach may lead to more accurate results, with the calculated RMSE against water level 28%–38% less than that produced by the source term coupling approach. The flux term coupling approach is therefore adopted to improve the current urban flood model, and it is further tested by reproducing the laboratory experiments of flood routing in a flume with partially open sluice gates, conducted in the hydraulic laboratory at the Zhejiang Institute of Hydraulics and Estuary, China. The numerical results are compared favorably with experimental measurements, with a maximum RMSE of 0.0851 for all the individual tests. The satisfactory results demonstrate that the flood model implemented with the flux coupling approach is able to accurately simulate the flow through hydraulic structures, with enhanced predictive capability for urban flood modeling.