Considered the current hydro-ecological conditions on Manas River basin and relevant existing problems，an evaluation index system consisting of three hierarchies and 19 individual evaluation indexes was established． The weight for each evaluation index was allotted based on the analytic hierarchy process (AHP)，and then the evaluation criteria and two-level comprehensive fuzzy evaluation method were deve-loped． The quality of the hydro-ecosystem in Manas River basin was evaluated as an example． The evaluation results show that the factors of hydrologic meteorology and eco-environment dominated the hydro-ecosystem quality in the basin; the memberships of the two categories to the class of very poor were 38． 4% and 47． 0%，respectively． At the same time，social-economic factor was relatively better，as its membership to the class of good was as high as 59． 2%． Overall，the hydro-ecosystems quality of Manas River basin was evaluated as low，which matched well with the fact． This suggests that the evaluation method developed in this study could have extensive application value in the similar areas．