Because lack of water resources in Manas river basin, the water resources carrying capacity evaluation is important to the water sustainable development. In this paper, we select the main factors of the water resources carrying capacity and separate into water resources subsystem, social subsystem, economic subsystem and ecological subsystem. Then established three evaluation models to evaluate the different years of water resources carrying capacity and made the application comparison. The fuzzy comprehensive evaluation model and matter-element models are adaptable to the water carrying capacity evaluation, but the determination of weights is too subjective; The projection pursuit theory is based on the sample characteristics of their own, and without given weight of each indicator, the results is more objective. The results show that the water resources carrying capacity in Manas River basin was at V1-stage in 2000; it is at V2- stage in 2010 and V3- stage in 2020, and then the water resources carrying capacity in Manas River basin is the ideal carrying capacity status. At the same time, because of saving water technological and industry restructure adjustment, water resources carrying capacity in Manas River Basin is on a benign trend. At last, some measures of improving the water resource carrying capacity were put forward.