Abstract: Ecological operation of water conservancy projects in polder area is an important measure to promote the ecological civilization in the field of water conservancy, and its scheme formulation is a multi-variable and multi-objective optimization problem. In order to explore a reproducible and extendable path for the formulation of ecological operation scheme of water conservancy projects in polder area of plain river network, taking Chengnan polder area in Wuzhong District of Suzhou City as an example, this paper summarizes the overall design idea of ecological operation scheme of water conservancy projects in polder area. With the help of water environment mathematical model, an optimization scheme is studied from the perspective of qualitative analysis and quantitative calculation. We suggest a general idea of determining the overall diversion and drainage pattern, then proposing an appropriate diversion scale, and optimizing the diversion and drainage control layout. The change rate of tank storage and the improvement rate of water quality can be used as comprehensive comparison indices to reflect the influence of the schemes on flood control and water environment. In the proposed scheme, Shihu Lake, Xiaoshi River and East Taihu Lake are used as water diversion sources, the Grand Canal is used as drainage destination, and the suitable diversion scale is 15 m3/s; by deploying scattered pumping stations along the canal to reduce the local operating water level, thus promoting the water flowing to the destination by itself. The proposed scheme has advantages of low storage disturbance and uniform spatial distribution of water quality improvement.