Water resources allocation is a key measure to alleviate the contradiction between supply and demand of regional water resources, as well as balance the relationship between water and development. Aiming at the relevant requirements of fine management of water resources in the new era, this paper takes agricultural, industrial, domestic and ecological water users as the research objects, and puts forward the calculation method of rigid water demand and elastic water demand based on the theory of stratified water demand and the existing achievements. Considering the social, economic and environmental benefits, an optimal allocation model of water resources for stratified water demand is constructed, and four benefit allocation schemes are obtained by NSGA-Ⅲ algorithm and the entropy weight method-technique for order preference by similarity to an ideal solution (EWM-TOPSIS) method. The Gini coefficient of water use is used to characterize the water use fairness between configuration units and water users, and the water use fairness of the configuration scheme in the non-inferior solution set is evaluated, by which the balanced configuration scheme that takes into account the fairness and efficiency of water use is selected. Finally, Ningxia Hui Autonomous Region is taken as a typical research area for the case application. The results show that under the balanced allocation scheme, the total water shortage in Ningxia in 2025 is 1.074×109 m3, the economic benefit is 218.26×109 yuan, and the pollutant discharge is 162.78 t. The Gini coefficient of water use in the whole region is 0.98, and the water use fairness between configuration units and different water users is quite high. Compared with the current year, the groundwater exploitation in the whole region corresponding to the balanced allocation scheme decreased by 0.091×109 m3, with a decrease of more than 16.1%, and the proportion of groundwater supply to total water supply decreased by 1.3 %, which further optimized the water supply structure of the autonomous region. The idea and method of balanced allocation of water resources proposed in this study can provide a reference for the balanced allocation of water resources in water shortage areas, and also provide a technical support for the implementation of the rigid constraint system of water resources in the new era.