The frequency of extreme wave events is increasing with climate change. The temporal and spatial variations of extreme wave height affect both human livelihood and the usage of ocean resources. The South China Sea and northern Indian Ocean both support coastal communities of high population density, with varied terrain structures and extreme wind and wave systems. This study focuses on the temporal and spatial variations of the extreme significant wave height in the South China Sea and northern Indian Ocean. Using nonstationary generalized extreme value analysis, trends for a 100-year return period of significant wave height were obtained for both. The most rapid increase in the 100-year return was found to be 0.015 m yr^-1 in the northern South China Sea and in the Arabian Sea; however, the 100-year return significant wave height fell in the mouth of the Bay of Bengal. After analyzing the possible causes and influence factors, we found that the increase in significant wave height in the northern South China Sea was dominated by local wind-waves and similarly, the Arabian Sea was affected by swell. The NINO3.4 index shows good correlation with the significant wave height in the northern South China Sea because typhoons are related to NINO3.4 in this area. The trends of the extreme wave height in the Arabian Sea and southern Bay of Bengal have good correlations with the South Asian summer monsoon index.