Abstract: The cities, population and wealth in Taihu Basin are highly concentrated, which sets higher requirements for the flood control. Assuming that the flood occurs in the basin and the typhoon lands in Shanghai, we analyze the impact of storm surge on flood control by using mathematical model. The storm surge will cause the rise of water level of the mainstream and upstream of Huangpu River and Northern Jiaxing area in a short time，in some area of Northern Jiaxing, the highest average daily water level and instantaneous water level will significantly exceed the warning level. The discharge of the flood is not smooth, which may cause floods and disasters in these areas. It is suggested that the government should improve the engineering system of the flood control, coordinate the flood control measures in the river basin, regions and cities, and seek for the maximum profit of the flood control by strengthening and improving the non-engineering measures.