With the continuous development of economy and society, the development and construction of cities is relatively strong. The capacity of flood water collection and drainage in town polder areas along the river cannot meet the requirements of economic and social development. In order to reasonably plan and improve the water system layout of town polder areas in combination with urban development and construction, taking Tuanjiewei in Pukou District, Nanjing as an example, by establishing the MIKE11 hydrodynamics model for river network, the model is used to calculate the water level and discharge of rivers in the polder area under different rainfall frequencies. The trial analysis of the planned river regulation scales and pumping station scales is made to give the waterlogging drainage dispatching scheme of the polder area. On the basis of adapting to the new situation of economic development and meeting the new requirement of water control, the water system in the polder area is systematically and perfectly arranged and planned, which can provide reference and experience for the water system planning of town polder areas along the river.