Sea level rise, strong typhoon and storm surge have increasingly serious impacts on coastal flood disasters in the southeastern China in the context of climate change. To address the climate change and estimate the hazard of extreme sea level in the future, based on the multiple data of oceanographic and atmospheric observation and methods of mathematical statistics, the impact of historical strong typhoon No.9914 (Dan) and No.1614 (Meranti) on the extreme sea level in coastal waters of Xiamen and estimates the changes and return of extreme sea level at scenarios of future sea level rise under RCP4.5 and RCP8.5 was analyzed in this paper. The results show that: (1) astronomical tide, storm surges and heavy precipitation induced the extreme sea level event (732 cm) during the period of strong typhoon No.9914; (2) the combined impacts of multiple hazards such as wind (ashore gale), rainfall (heavy precipitation), waves (giant waves), tides (high tide) and current (torrents) is an important cause of serious disasters in coastland of Xiamen; (3) under the medium and high greenhouse gas emission scenarios (RCP4.5 and RCP8.5), by 2050 and 2100, recent 1-in-100-year extreme sea level event will become 1-in-30-year (1-in-2-year) and 1-in-25-year (1-in-less than 1-year). It shows that the hazards of extreme sea level on coastland of Xiamen will increase significantly, and high adaptation measures in Xiamen should be taken to reduce the risk on coastal flood hazards in the future.