In the design of ecological river comprehensive improvement projects, the MIKE11 software is used to build the one-dimensional hydrodynamic model to numerically simulated the waterlogging drainage level of ecological river, and compare and analyze the changes of maximum waterlogging drainage level and the duration of high water level before and after river improvement in order to assess the implementation effect of various comparative measures for improving the waterlogging drainage capacity of river in the comprehensive improvement engineering of ecological rivers. The results show that the MIKE11 model had a good effect in simulating and calculating the waterlogging drainage level of river in polder areas, and can be used to improve the reliability and efficiency of similar engineering designs. The simulation results can provide some technical references for the design of comprehensive improvement engineering and the daily operation and scheduling management of ecological rivers.