Based on the characteristics that the short water resources in total, uneven distribujtion of interannual and annual water, and serious water pollution in the Malianhe River Basin, a large system and multi-objective water resources optimal allocation model was set up with the theory of system analysis and optimization technology. And the optimal allocation scheme under the expected water allocation conditions in 2020 was obtained using the method of optimized NSGA-II. The results show that the total water supply is 57 086×104 m3 , water supply for industry is 21 690×104m3 (the total output value is about 14.46 billion Yuan), water supply for energy production is 4 329×104m3 (the total output value isabout 3.4632 million Yuan), and water supply for agriculture, domestic and ecology is 20 840×104m3, 9 452×104m3, and 811×104m3 espectively.Comparing the optimal allocation scheme with the expected solutions, the total water supply is increased by 6 710 ×104m3, and the water shortage rate is decreased by 11.41%. Finally, integrated management research was completed according to the results of supply and demand balance analysis. Under the condition of the optimal water allocation scheme for 2020, the industry water shortage rate is 3.21% which is de -creased by 4.51%, energy production base water shortage rate is 0.00%, agriculture water shortage rate is 4.64% which is increased by 26.17%,domestic water shortage rate is 0.00%, and ecology water shortage rate is 1.00% which is increased by 1.00%. The optimal allocation schemeachieved the best water distribution, which made the precious and limited water resources provide maximum social, economic and environmen -tal benefits, and provide water resources supports for the rapid growth of economic and energy industry in the Malianhe River Basin.