[Objective] The dynamic changes of water resource carrying capacity in agro-pastoral ecotone is analyzed, which will provide a theoretical reference for the sustainable development of the similar areas. [Methods] The study selects the Horqin District, Tongliao City in Inner Mongolia as a case study area, which is characterized with typical characteristics of agro-pastoral ecotone. Through the method of system dynamics simulation, we established the system dynamic model for the coordinated development of “society-economy-ecology” based on the limited water resources in Horqin District. Meanwhile, according to the characteristics of agro-pastoral ecotone and social economic development in Horqin District, five theoretical models of regional “society-economy-ecology” coordinated development were put forward, including natural growth model, primary industry-modernization model, secondary industry-dominated model, tertiary industry-led model and recycling economic development model. [Results] On the basis of system dynamic simulation, we used genetic projection pursuit method to optimize the simulation results, and found that the recycling economic development model was the model with optimal water resources carrying capacity.[Conclusion] (1) The proper arrangement of agricultural and pastoral proportion is a key to saving limited water resources in agro-pastoral ecotone; (2) The development of traditional industries in agro-pastoral ecotone would cause water resources scarcity; (3) Recycling economy is an effective way to improve the carrying capacity of water resources in agro-pastoral ecotone; (4) The increasing investiment on researches on the carrying capacity of water resources in agro-pastoral ecotone will help to provide the support for regional sustainable development.