In order to study the water risk of rainstorm waterlogging in flood protected zone and redue the loss of flood disaster, the paper calculated water area and water depth value of rainstorm waterlogging based on GIS and SWMM model so as to carry out flood risk analysis. The method was applied in the calculation of rainstorm waterlogging in Cinanfeizuopian flood protected zone. The observed precipitation water levels of Yong xing penstock，Jia river penstock and Youth penstock in 2007 were used to verify the runoff model. The results show that the absolute errors of calculated water level in three positions are respectively 0.02，0.1 and 0.14 meters. The calculation result is more reasonable.The model was applied to the risk analysis design of rainstorm waterlogging once every 20 years in flood protected zone.The result can play a vital role in risk management and decision.