：The ecological environment of the agro-pastoral ecotone in Northwest China is extremely fragile. Due to global warming, the frequent droughts in this region have seriously affected agriculture and animal husbandry, which is not conducive to the sustainable socio-economic development of the agro-pastoral ecotone there. It is the special location and ecological value that determine the region has an important strategic significance in socio-economic development and ecological environment protection in China. The usage of land resources plays an important role in not only the ecological environment, but the socio-economy. Therefore, the purpose of this paper is to achieve ecological environmental protection and economic development by optimizing the allocation of limited land resources in the region. The application of multi-objective genetic algorithm and FLUS model can improve the land use optimization configuration from many aspects (i.e., quantitative structure, spatial distribution, comprehensive benefits). In addition, the combination of the genetic algorithm and multi-objective programming model can provide more alternative options for it. In this paper, the multi-objective genetic algorithm and FLUS model are used to simulate the land use change of the region in 2025. By setting up four scenarios (i.e., natural development, ecological protection priority, economic development priority and eco-economic equilibrium), we explore how to optimize land use allocation on the condition of considering both the protection of ecological environment and the development of social economy. The results suggest that the eco-economic equilibrium optimization scheme shows great advantages in both the quantitative structure and spatial distribution of land use types, and its comprehensive benefits are superior to the other three scenarios. On the premise of reasonably limiting the speed of economic development, this scenario has enabled the ecological construction to develop at stable speed. Its economic benefits have increased by 8.96% compared with those under the ecological protection priority scenario, and its ecological benefits have increased by 0.77% compared with those under the economic development priority scenario. The scenario achieves the coordination between ecological protection and economic development.The eco-economic equilibrium optimization scheme has shown great potential in many aspects, such as promoting the development of unused land, assisting in the adjustment of land use structure, and driving the optimization of industrial structure. The optimal allocation of land use provides decision-making assistance for the future ecological environment construction and economic development planning of the agro-pastoral ecotone in this region. In addition, to solve the contradiction between economic development and ecological construction in the agro-pastoral ecotone, the government should strictly co-ordinate arrangements for various types of land, while enhancing the comprehensive utilization of land resources.