Adopting optimum control and scientific management of eco-environment is very important to protecting eco-environment against disruption and promoting the coordinated growth of soc-economy system and eco-environment system and building a harmonious relationship between human behavior and natural world, especially in the arid region, western China. According to the characteristics eco-environment of small basin in arid region, from the point of overall development of small basin, introduces the theory framework of eco-environmental control, and puts forward a new control model, and gives a case study: Bosten Lake Basin in Xinjiang China. The a good example for eco-environmental control in arid region had been provided.