Disastrous storm surges and waves caused by typhoons are major marine dynamic disasters affecting the east China coast and the Changjiang River Estuary, especially when they occur coincidentally. In this study, a high-resolution wave–current coupled model consisting of ADCIRC (Advanced Circulation) and SWAN (Simulating Waves Nearshore) was established and validated. The model shows reasonable skills in reproducing the surge levels and waves. The storm surges and associated waves are then simulated for 98 typhoons affecting the Changjiang River Estuary over the past 32 years (1987–2018). Two different wind fields, the ERA reanalysis and the ERA-based synthetic wind with a theoretical typhoon model, were adopted to discern the potential uncertainties associated with winds. Model results forced by the ERA reanalysis show comparative skills with the synthetic winds, but differences may be relatively large in specific stations. The extreme surge levels with a 50-year return period are then presented based on the coupled model results and the Gumbel distribution model. Higher risk is presented in Hangzhou Bay and the nearshore region along the coast of Zhejiang. Comparative runs with and without wave effects were conducted to discern the impact of waves on the extreme surge levels. The wave setup contributes to 2–12.5% of the 50-year extreme surge level. Furthermore, the joint exceedance probabilities of high surge levels and high wave height were evaluated with the Gumbel–logistic statistic model. Given the same joint return period, the nearshore region along the coast of Zhejiang is more vulnerable with high surges and large waves than the Changjiang River Estuary with large waves and moderate surges.