The spatio-temporal variations of significant wave height and its extremum in the northern South China Sea from 1996 to 2015 are analyzed based on the wave hindcast simulation by the third-generation wave model WaveWatch III (WW3). Two extreme value distribution methods, Pearson-III and Gumbel methods, have been used to estimate the return period of the extreme significant wave height in the northern South China Sea. The results show that the seasonal variation and spatial distribution of significant wave height in the northern South China Sea are consistent with the monsoon field, similar to the results of reanalysis data. It is high in autumn and winter and low in spring and summer, and decreases from the west part of the Luzon Strait to the southwest. But the extremum of significant wave height is strongly affected by the temporal resolution. The higher resolution (such as hourly), the more typhoon wave characteristics are displayed. After deducting the seasonal cycle signal, both the significant wave height and its annual extremum show an intense linear trend, increasing by 7.7% and 31.6% in the last 20 years respectively. There are several large value regions of the return period wave height in this area. They are related to the typhoon's track and intensity directly, indicating that typhoons are the primary mechanism causing extreme waves in this region. Comparing the Pearson-III and Gumbel distribution, it is found that if the extreme significant wave height was relatively low and the frequency decreased slowly with the growth of the extremum, the two methods are both accurate, with little difference which could be ignored. However, when the extreme significant wave height was much higher in one year than that in other years, the estimated result of the Pearson-III would be much higher than that of the Gumbel method, and also closer to the actual value. In other words, the Pearson-III extreme value distribution behaves better in this situation. This study shows that when the extreme significant wave height caused by a super typhoon is much higher than that in other years, the estimation from different methods differs greatly, which will significantly affect the assessment of the return period. Besides, the strong increasing trend of the extreme significant wave height in the northern South China Sea will also bring a non-negligible impact on the calculation of return period wave height and marine engineering protection in the future.