[Objective] The conflicts between water supply and demand, overexploitation of groundwater, and ecological water consumption in the Baiyang River basin in Xinjiang Wei Autonomous Region was evaluated, and the water supply areas of the basin were taken as the research objects to optimize the allocation of water resources for the basin in order to provide a reasonable basis for the healthy development of the economy and the allocation of water resources. [Methods] A comprehensive evaluation model of water resources was used to analyze the water resource carrying capacity of the Baiyang River basin, Daban District, and Tuokexun County. Thus, a multi-objective function model providing for the smallest water shortage, the largest economic benefit, and the best fairness was established. A second-generation non-dominated sorting algorithm (NSGA-Ⅱ) was used to solve the problem. Through the optimization of the results, the optimal water distribution plan was obtained. [Results] The comprehensive evaluation index of the Baiyang River basin was 1.0. After the planning year (2030) when the allocation of water resources was optimized, water consumption decreased by 23.7% (compared with the predicted results of the ARIMA model) and 9.9% (compared with the planned water distribution plan), and GDP increased by 10.5% and decreased by 1.4% respectively. The fairness of water distribution in the basin changed from a wide variation to an absolute average. [Conclusion] The water resources of the Baiyang River basin are currently on the verge being overloaded and slightly uncoordinated. Optimal allocation of water resources could produce the efficient use and reasonable allocation of regional water resources.