Based on the principle of optimal allocation of water resources, a bi level optimization model was developed, which take the economic benefit as the upper level objective and the environmental benefits as the lower level objective. Using the lingo software and fuzzy satisfaction approach, the multi objective problem was transformed into a single objective problem, and the water resources of Changshu city were configured. The results show that the economic benefits of the regional water resources allocation system would amount to 24.84×108 and 27.89×108 yuan, the total water resources distribution would achieve 86228×104 and 93809×104 m3, and COD emissions would reach 8342 and 9450 t in 2020 and 2030, respectively. Moreover, the Yangtze River water intake accounted for 73% of the total water distribution, and the trend gradually increased. Comparing the bi level optimization results with the two main objective optimization results can provide the decision making plans under different scenarios.