To address the issue that current coupled surface water flow and pipe network flow models are mostly based on structured grids, making it difficult to adapt to complex coastlines and urban boundaries, a real-time bidirectional dynamic coupling model, FVCOM-SWMM, was developed based on the open-source unstructured-grid hydrodynamic model FVCOM and the pipe network hydrodynamic model SWMM. The reliability of the proposed model was verified by comparing its results with those from commercial software and physical model experiments. The simulated results of a rain-tide coincident event in a coastal urban area with tortuous coastlines and complex building layouts show that the model can be used to simulate flooding processes in urban areas with complex boundaries under storm surge conditions.