The seasonal and interannual variabilities of sea surface wind (SSW) in the South China Sea (SCS), especially in coral reef regions such as Nansha Islands, Xisha Islands, Zhongsha Islands and Dongsha Islands were investigated in detail using the Blended Sea Winds dataset (1988–2017). Annual and monthly variations of SSW and sea surface temperature (SST) in the four zones were investigated. Empirical Orthogonal Function (EOF) analysis of wind field was performed to aid in better understanding the different spatial patterns. The results indicate that, as observed in the spatial distribution of the first mode of monthly mean wind speed anomaly, the magnitudes in the four island zones are all negative and are similar to each other, showing that the variations of SSW in the four island zones are consistent. In the second mode, the magnitudes in Nansha Islands are opposite to those in the other three zones. The spatial distribution of the third mode reflects regional differences. The maximum annual SSW appears in Dongsha Islands, and the minimum appears in Nansha Islands. The interannual variations of SSW in all island zones are basically concurrent. The island zones with high SSW mostly have low SST, and vice versa. There may be an inverse relationship between SSW and SST in coral reef regions in the SCS. The multi-year monthly variations of SSW in the island zones present a ‘W’-shaped structural variation. Each island undergoes two months of minimum SSW every year, one during March–May (MAM) and the other during September–November (SON). Both months are in monsoon transition periods. During the months with low SSW, high SST appears. The SST peaks almost correspond to the SSW troughs. This further indicates that SSW and SST may have opposite changes in coral reef regions. Coral bleaching events often correspond to years of high SST and low SSW.