With accelerated urbanization processes, water quality deterioration and ecological decline in plain river network areas caused by high pollution loads, weak hydrodynamic conditions, and strong artificial intervention, have become bottlenecks for urban development. Combining the hydrological and hydrodynamic characteristics of highly urbanized area of Lake Taihu Basin, a water quantity and quality coupling model was constructed. Considering multiple objectives, i.e., water quality improvements, hydrodynamic improvements, and economic costs, a multi-criteria decision making comprehensive evaluation system for water transfer, comprising target, index, and element layers, was established. Based on the fuzzy analytic hierarchy process (FAHP), the weights for water quality improvement, hydrodynamic improvement, and economic cost index layers in the comprehensive evaluation system were 0.390, 0.345, and 0.265, respectively, and the corresponding element layers were designed for each index layer, in which a total of 10 elements were included. The decision making in the comprehensive evaluation system, including different water transfer schemes, is then evaluated using the fuzzy comprehensive evaluation (FCE) method. The results showed that the FAHP-FCE could effectively determine the optimal water transfer scheme for multi-objective decisions on water quality improvement, hydrodynamic improvement, and economic cost under different scheduling scenarios. The regional controlled projects had much greater impacts than that of the projects controlled by Xishan District in the highly urbanized area of Lake Taihu Basin, and the dispatching mode of Urban Flood Control Enclosure had the greatest influence on the effect of water transfer in Xishan District among the regional controlled projects. Water quality compliance rate for the optimal water transfer scheme achieved in the study area was 82%, average rate of water quality improvement was 31%, and proportion of cross-sections meeting the Class Ⅲ water quality standard was 61%. Average flow velocity was 0.10 m/s, proportion of the optimal velocity was 39%, and proportion of stagnant sections was 32%. The multi-criteria decision making comprehensive evaluation method based on FAHP-FCE and used to determine the optimal water transfer scheme, was more comprehensive and reasonable than the traditional single- or multi-indicator simple comparison results, and can provide a reference for highly urbanized plain river network areas, especially for Lake Taihu Basin, for water transfer to improve the water environment.