According to the topography, geomorphology, and drainage system of the Putian coastal area, the Putian Coastal StormSurge TorrentialRain Waterlogging Simulation Model is established, aiming at the influence of both storm surge and typhooninduced torrential rainfall. Using the area rainfall calculated with the quantitative estimation of precipitation using radar and AWS’s, and the boundary conditions of the model based on the dynamic water level set at the coastal border and the estuary, the operational experiment for the risk assessment of storm surge disaster in Putian area was carried out during Typhoon Nanmadol. The model is used in experimental research for the storm surge caused by Typhoon Nanmadol on 1 September 2011. These simulation results are directly used in contrasting and assessing the actual disaster caused by Typhoon Nanmadol. The simulation results are close to the actual disaster, which will lay a foundation for risk assessment and division on the typhoon and torrential rain scenarios.