With the rapid expansion of the scale of deep sea net-cage use in the nearshore area of Hainan Island, tropical cyclone-induced wave hazard assessment is urgently needed. In this study, the wind-wave-current coupled ADCIRC?+?SWAN model, which considers the effects of tidal and storm surges, was used to simulate tropical cyclone events over the last 33 years. This model adopts an unstructured high-resolution grid with a nearshore resolution of up to 100 m. The compared simulated results and observations during typhoons JEBI (2013), HAIYAN (2013) and KALMAEGI (2014) were in agreement. This study statistically analyzed maximum significant wave heights on the basis of a large set of simulated storm wave level maps to derive the wave heights of different return periods. Then, the results of nearshore wave hazard classification were obtained by applying the affinity propagation (AP) clustering method to dozens of nearshore profiles. The results demonstrate that the risk at any point in the nearshore area of Hainan Island is dominated by the wave hazard type and water depth condition. The wave hazard assessment method developed for Hainan Island will be significant in assisting government decision-making in the rational planning of deep sea net-cage aquaculture.