The extreme sea conditions caused by typhoons pose a threat to the design safety of marine and coastal engineering structures. In the past, design wave height calculation models that only considered the frequency of typhoons ignored the influence of other hazard factors of typhoons, resulting in lower design standards. In this paper, typhoon frequency, intensity, and distance are selected, and dimensional influences of different factors are eliminated through standardization processing. Based on the correlation between different hazard factors, we have obtained a multi-dimensional discrete joint probability distribution of typhoon hazard factors and constructed a new design wave height that considers the comprehensive effects of typhoon frequency, intensity, and distance. Our results show that the design wave height values of the 50-year, 100-year, and 200-year events are 12.59%, 8.10%, and 3.14% higher than the Gumbel distribution, which is more in line with the distribution of the wave height of waves under severe typhoon conditions. The new model can fully reflect the impact of typhoons on wave height, which can provide a reference for the design safety of marine engineering in the South China Sea.