Based on the third-generation wave model WAVEWATCH-III (WW3), this paper analyzes the changing trend of wave power density (WPD) in the South China Sea, which can provide necessary references for the development and utilization of wave energy resources in the future. In this study, multi-platform cross-calibrated (CCMP) wind data was used to drive WW3 to calculate the WPD of the South China Sea. The Mann-Kendall (MK) algorithm can be used to determine the mutation of WPD, and the accuracy of the CCMP wind was verified. Next, the time distribution of WPD is analyzed for the whole sea area and dominant sea area of the South China Sea, and on this basis, the dominant sea area for the development of wave energy resources in the South China Sea was studied. The results are as follows: (1) Extreme weather has a significant impact on the change of WPD in the South China Sea, and this change is likely due to the effect of extreme weather on sea temperature. (2) Dongsha Islands has the highest annual WPD value and has the greatest impact on the overall trend change of the South China Sea. (3) Integrated wave energy exploitability and safety and technology perspectives, the waters around Taiwan Strait are more suitable as the primary site for energy conversion.