This study mainly aims to hindcast historical Typhoon Nepartak (2016) and to analyze tide–surge and wave interactions. To achieve this goal, a coupled tide–surge–wave model was built around the coast of Taiwan, and it was applied to simulate storm surges and waves during historical typhoon event. To demonstrate its capability, the coupled model was validated with observed water levels, wind speeds, atmospheric pressures, wave heights, and wave periods at different stations. Quantitatively, the model results reasonably reproduced the observed data. Furthermore, the model was utilized to explore the tide, surge, and wave interaction using historical Typhoon Nepartak (2016). The model results revealed that onshore wind enhanced the surge height, while offshore wind decreased the surge height. The atmospheric pressure consistently displayed a positive contribution to surge height. The wind-induced surge height contributing to the total surge height was 136.83% at Taichung Harbor, because the offshore wind mainly dominated the surge height compared to the effect of atmospheric pressure. The atmospheric pressure-induced surge heights contributing to the total surge height were 100.59%, 96.26%, and 99.74% at Kaohsiung Harbor, Hualien Harbor, and Taitung Fugang, respectively, as a result of the atmospheric pressure dominating the surge height. However, the contribution of the wave setup to the total surge height was minor. The path of typhoons at different time frames significantly affected the spatial distributions of surge height and wave height around the coast of Taiwan. The contributions of water level and current to wave height reached a maximum value of approximately 0.3 m at Suao, while the contributions at Penghu, Qigu, and Eluanbi were all less than 0.2 m. This signified that the influence of the water level and current on wave height was not negligible.