In order to optimize the allocation of water resources of the Henan Section of the Yangtze River to Huaihe River Water Diversion Project, the optimal allocation model of water resources with the maximum economic benefit, the minimum water shortage and the minimum pollutant emission as the objective function was constructed. The improved third generation non-dominated sorting genetic algorithm (A-NSGA-Ⅲ) was used to solve the model, and four optimal allocation schemes of water resources focusing on different objectives were selected. The results show that the water diversion from the Yangtze River to the Huaihe River can greatly alleviate the contradiction between supply and demand in the water-receiving area. The water shortage rate can be reduced to 10.43% and 5.47 % in 2030 and 2040, respectively. The water supply structure can also be optimized and the ecological environment can be improved. The fourth scheme with the largest coupling economic-social-ecological environment coordination degree is the optimal scheme. Under the fourth scheme, the proportion of groundwater supply in the planning years can be decreased by to 53.32% and 46.59%. The A-NSGA-Ⅲalgorithm has good applicability in solving multi-objective and high-dimensional water resources allocation problem, which can provide reference for the formulation of water resources allocation scheme in the Henan Section of the Yangtze River to Huaihe River Water Diversion Project.