Water diversion is a significant method to improve the water environment in the plain river network area. Through building up the one-dimensional hydrodynamic and water quality model of the plain river network area of southeast Zoumatang of Taihu Basin, the effect on water environment of different water diversion schemes was simulated, and the heterogeneous factors in the process were determined. A multi-objective function and evaluation system combining environmental benefits and economic benefits were constructed from three aspects, including decision-making, water quality indexes and spatial indexes, and the water diversion schemes were evaluated and optimized. The results show that: (1) With a larger flow, water diversion can improve the regional water environment to some extent. After 5 days of water diversion under the planning schemes, the average improvement rates of COD_Mn, ammonia nitrogen and total phosphorus were 30.7%, 22.2% and 26.4%, respectively. (2) Heterogeneity existed in the process and effect of water quality improvement in different spatial points and water quality indexes in the river network during water diversion. (3) The water quantity and dispatching mode of water diversion as well as distribution of pollutants all have different effects on the water quality in the river network. (4) Compared with the existing method, the multi-objective evaluation system of water diversion established in this research can effectively cover the heterogenous factors and evaluate and optimize different water diversion schemes from multiple objectives, therefore can achieve comprehensive optimization and control of water quantity and quality, and provide theoretical reference for long-term management and scientific decision-making of water environment in the plain river network area.