The spatio-temporal variations of the significant wave height (SWH) in the Western North Pacific and South China Sea (WNP-SCS) region, as well as their driving mechanisms, are investigated based on the long-term (1981–2014) simulation by a coupled ocean–atmosphere model and a WAVEWATCH III model. The Empirical Orthogonal Function modes of SWH anomalies show different patterns in the cold and warm seasons. In winter, the first mode (explaining 40.63% of the variance) shows a monopole pattern with large loadings lying in SCS and the WNP to the east of the Philippine Islands, which is primarily associated with the El Niño-Southern Oscillation (ENSO) on inter-annual time scales. The second mode (explaining 19.62% of the variance) shows a dipole pattern with negative loadings in the northeastern SCS and positive loadings to the east of Japan, which is prominently connected with the intensity variation and longitudinal shift of Aleutian Low on decadal time scales. In summer, the first leading mode (explaining 73.47% of the variance) presents large loadings located mainly in the WNP region between 10° N and 30° N and secondarily in the central SCS, which is associated with the ENSO-affected tropical cyclone activities and South China Sea summer monsoon, respectively.