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Tropical cyclone (TC)-induced coastal flooding can lead to severe hazards in low-lying lands and is expected to be exacerbated by sea level rise and TC climatology changes related to the warming climate. Since the dense population in Xiamen Bay, Fujian, China, it is highly valuable in understanding coastal flooding of it, but little studies involved this topic. In this study, we establish a high-resolution numerical model covering all coastal low-lying land in Xiamen Bay based on FVCOM. This model is then used to assess the flood risk in Xiamen Bay under TCs with 10-, 100-, and 1000-year pressures by applying a multi-tracks blend method. The results show that 126 km2 of low-lying area can be flooded periodically by astronomical tides; and 388, 504, and 598 km2 of low-lying area can be flooded under TCs with 10-, 100-, and 1000-year pressures, accompanied by increased average flood depths of 2.3, 2.8, and 3.4 m, respectively. By 2100 under SSP5-8.5, the well-protected Xiamen Island becomes impacted by TCs with 10-year pressure, and flood areas under TCs with 100-year pressure are estimated to be nearly equivalent to that under TCs with 1000-year pressure at the current climate. The most increased exposure area by climate change are artificial surfaces and agricultural areas, showing the potential higher flood disasters in future.