Using weather， physical geographic and socio economic data of Nanning, four indexes of natural disaster making factors are constituted: susceptibility, disaster hitting environment sensitivity, disaster bearing object vulnerability, and disaster prevention and reduction capability. With GIS technology, the rainstorm and flooding risk assessment index system is established, and the rainstorm and flooding risk of Nanning was zoned in 1000 m×1000 m cells. Results show that the area with the highest risk of storms and flooding disasters is Binyang.Thereinto, the most seismic risk area is in the north and east of Binyang, and the most fragility area is in the middle of Binyang, as well as southeast of Hengxian. The zoning result reveals the distribution of potential risk of rainstorms and flooding disasters in Nanning. Key disaster prevention measures for rainstorms and flooding disasters should focus on the high risk area.