In this study, the numerical wave model Simulating Waves Nearshore (SWAN), which resolves nearshore wave processes, and a hydrodynamic model, the Finite-Volume Community Ocean Model (FVCOM), were coupled to simulate waves and currents during Typhoon Fung-wong (2014) and Typhoon Chan-hom (2015) around the Zhoushan Islands. Both of these models employ the same unique unstructured grid. In particular, the influence of sea-surface currents, e.g., typhoon-induced and tidal currents, as well as the sea-water level, on wave simulation was studied. The composite wind field, which is derived from the parametric Holland model and European Centre for Medium-Range Weather Forecasts (ECMWF) winds (H-E winds), was taken as the forcing field. TPXO.5 tide data, sea-surface temperatures from the HYbrid Coordinate Ocean Model (HYCOM), HYCOM sea-surface salinity, and HYCOM sea-surface current were treated as open-boundary conditions. The comparison of sea-surface-current speed between the FVCOM simulation and the National Centers for Environmental Prediction (NCEP) Climate Forecast System Version 2 (CFSv2) data revealed a root-mean-square error (RMSE) of about 0.1206 m/s, with a correlation (Cor) more than 0.8, while the RMSE of the simulated sea-water level when compared with the HYCOM data was around 0.13 m, with a Cor of about 0.86. The validation indicated that the simulated results in this study were reliable. A sensitive experiment revealed that the sea-water level affected the typhoon-induced wave simulation. Validation against the measurements from the moored buoys showed an RMSE of <0.9 m for the sea-water level, which specifically reflected less overestimation during the high-sea state. Moreover, the significant-wave-height (SWH) difference (SWH without the sea-water level minus SWH with the sea-water level) was as great as −0.5 m around the Zhoushan Islands during the low-sea state. Furthermore, we studied the typhoon-induced waves when Typhoon Fung-wong passed the Zhoushan Islands, revealing that the reduction of SWH could be up to 1 m in the Yangtze Estuary and tidal flats when the maximum waves occurred.