There are a large number of people, factories, farmlands and buildings in Huainan area, the south part of Huai River. Big floods will severely endanger people ' s life and property. In this paper, HEC---RAS software and HEC-GeoRAS module are employed in GIS to simulate the flood overtopping inundation in Huainan reach of Huai River under the existing flood protection works during floods once in 40, 60, and 100 years respectively. The designed water level of different cross-sections, the overtopping inundation area, and the inundation depth data are obtained. The simulation manifested that the flood protection works in this reach are capable of handling floods once in 40 and 60 years, and can generally withstand floods once in 100 years. The simulated water level is consistent with the designed level. Therefore it is concluded that it is reasonable and credible to use HEC-RAS to simulate flood overtopping, and thereby providing reference for the early warning, the population evacuation planning, as well as flood disaster risk analysis.