An agro-pastoral complex system has functions of integrating resources and considering the balance between ecology and livelihood, and that between environmental protection and economic development at the same time. Establishing an agro-pastoral complex system is the only way to shake off poverty and enrich people's life. It is urgent to establish a sustainable operation mechanism in the practice of agro-pastoral combination at present. The present study accordingly analyzed the resource support, production mode, and material flows of the agro-pastoral complex system in the Wanjigou village, Yanchi County, Ningxia by using the different methods including household surveys, soil nutrient determination, farming and animal husbandry yield measurements, and compartment model building. Results showed that the main factors which accelerate the development of the agro-pastoral complex system were the foundations of the resources and the production mode coupled by cultivated land, bush land, and the grassland system. At present the sustainability of the water resource in the irrigated land which mainly produces the forage and that of the water resource in the bush land of Caragana were the key factors of maintaining the long-term sustainability of the agro-pastoral complex system. The inevitable choice for the sustainable development of the agro-pastoral complex system in agro-pastoral ecotone is to enhance the systematic regulation and the integrated synergy between soil and water resources, forage production, and Tan sheep production.