In this paper, according to the limitation of the traditional water resources carrying capacity evaluation method and instability of strong jump in evaluation result, carrying capacity of water resources quantitative evaluation index was established and improved based on the characteristics of complex system in the basin. The comprehensive empowerment was introduced into the index, and variable fuzzy assessment was improved furthermore. The established assessment model of regional system carrying capacity was applied in Yarkant river basin. The comparison result of different evaluation methods shows that the regional system carrying capacity is level 2-3 which is close to the saturation, and there is a serious contradiction between supply and demand. The utilization rate of basin water resources is improved in the planning year. The carrying capacity in the planning year is level 2 with a decreasing trend in primary industry and increasing trend in water utilization rate. The supply and demand contradiction is alleviated in the planning year. The division of evaluation grade is obvious and objective, and the grade jump phenomenon is avoided, which provided reference in watershed planning and supply and demand rationing of basin water resources.