Water is the basic, predominent and controlling element of economic and social development. The bearing space of water determines the scope of economic and social development, and the shortage and unbalanced spatial distribution of water resources are the prominent contradictions in northern China. Based on the conventional water resources allocation, and the objective function and constraints of spatial equilibrium, the idea of “spatial equilibrium” water control was introduced to construct a double layer multi objective allocation model of water resources with spatial equilibrium, economy, society and ecological environment as the objective functions and spatial equilibrium, available water supply and positive variables as the constraints, and then the improved genetic algorithm was adopted to solve the model. The application of this model to the research of the rational allocation of water resources in Horqin District, Tongliao City, Inner Mongolia show that the spatial equilibrium level of water resources in the planning year is significantly improved, the overall spatial equilibrium degree of water resources will increase from 0.40 in the current year to 0.71 in 2025, and the spatial equilibrium level will reach the quasi balanced level. In 2030, the overall spatial equilibrium degree of water resources will continue to increase to 0.83, reaching the basic equilibrium level. The research results enriched the approaches of water resources allocation, which will not only provide technical support for the fine management of water resources in Horqin District, but also provide references for the planning and allocation of water resources in the arid areas of northern China.