Abstract: The accelerating process of urbanization and the intensification of human activities have not only caused a series of impacts on the urban water environment, but also increased the pressure of urban flood control and drainage. In order to explore the impact of the adjustment of urban water system layout on urban flood control and drainage and the solution to the deterioration of urban water environment, taking the high- speed railway new town in Yixing City of Jiangsu Province as an example, the original water system layout is adjusted and optimized. The hydrological and hydrodynamic model of the high-speed railway new town after water system optimization is built by using MIKE11, and the maximum water level of each main river channel before and after water system layout optimization is compared to analyze the impact of water system layout on urban flood control. It also puts forward feasible ideas for water diversion and distribution in the region, determines the scale of water diversion and distribution project, and provides solutions for the deterioration of urban water environment.