Tropical cyclones may be destructive in the coastal region, such as the Gonu tropical cyclone, which affected the Arabian Peninsula and parts of southern Iran in 2007. In this study, a coupled MIKE 21/3 HD/SW (hydrodynamic/spectral wave) model was used to simulate the inland flooding inside the Sur port during the Gonu tropical cyclone. The MIKE 21 Cyclone Wind Generation (CWG) tool was utilized to generate the cyclone’s wind and pressure field. The required input data were obtained from the International Best Track Archive for Climate Stewardship (IBTrACS) and imported into the CWG tool. In this study, the wind and pressure fields were compared between the analytical vortex model and European Centre for Medium-Range Weather Forecasts (ECMWF) data during the Gonu cyclone passage. Moreover, by developing a new model, artificial Mangroves’ effect on inland flooding was investigated. The results show that, contrary to the ECMWF data, the analytical vortex models well captured the storm event’s wind and pressure field. Furthermore, the flood hazard is calculated based on the inundation depth, flow velocity, and area’s vulnerability. The flood hazard map shows that 5% of the coast is at high-risk, 49% is at medium-risk, and 46% is at low-risk class in the Sur port. By applying Mangroves as flood risk reduction, the high-risk area is almost completely removed. However, medium and low-risk zones increase by 50% and 50%, respectively. This information could be helpful in disaster risk reduction and coastal management in the future.