A real-time two-way coupled atmosphere-wave model in the South China Sea (SCS) has been established based on the atmosphere model WRF and the wave model SWAN in this study. We implement a nested computational grid along the SCS in the SWAN model and utilize the WRF model to provide high-resolution mesoscale wind field and pressure field over the SCS under the influence of typhoons. The numerical simulation of the typhoon waves generated by typhoon Kai-tak (1213), Rammasun (1409) and Hato (1713) had been carried out. The results of the numerical simulation are compared with the results of the field observation and the satellite altimeter. The verification results show that the coupled WRF-SWAN model has a high accuracy in the simulation of typhoon waves under the influence of typhoons in the SCS. The results of the simulation reveal the asymmetrical distribution of wind speed and typhoon wave height generated by typhoons in the space. The intensity of the typhoon on the right is greater than that on the left of the typhoon track. The real-time two-way coupled atmosphere-wave model based on the WRF model and the SWAN model can accurately simulate the dynamic process of typhoon and the temporal and spatial distribution of the typhoon waves generated by typhoons. According to the results of the coupled WRF and SWAN model, a corresponding relationship between typhoon wind speed and wave height was obtained, which was combined with the statistical data of typhoon occurring in the SCS during 1949–2019, the distribution characteristics of typhoon wave in the SCS had been simulated. The statistical data grid with a spatial accuracy of 0.5 degree of typhoon waves in the SCS had been established, and then the statistical wave height of typhoon in the SCS based on the Pearson-III distribution had been simulated. Eight characteristic locations have been identified in the SCS, the highest frequency and the hugest height of typhoon wave is near the Luzon Strait, the average of typhoon wave height is reached 9.2 m. The second is southern Taiwan in the eight different selected positions, and the statistical average value of typhoon wave height is close to 8.0 m. Comparison of the Paracel Islands, Spratly Islands and Dongsha Islands, the smallest statistical value of the typhoon wave height is the waves in Spratly Islands, with a mean value of 3.0 m, and the statistical mean value of typhoon wave height near the Paracel Islands and Dongsha Islands are about 6.0 m. Based on the statistical results, combined with the frequency of typhoon in the region, the distribution of typhoon wave height can be calculated at any location in the SCS, and it can be provide to some references for the design of the coastal and ocean engineering.