Shulehe river basin belongs to extremely arid desert climate, and the formation and storage of its water resources is more difficult, the environment of water ecology is fragile. In order to strengthen analysis of water resources, improve water use efficiency, develop and utilize water resources more rationally, the paper used PCA method , and selected the typical section of three reservoirs from upper, middle and lower reaches of Shulehe river basin to analyze and evaluate water quality.The results are that the water quality in Shuangta Reservoir belonged to grade I before 1997. The water quality of Shuangta reservoir dropped to grade Ⅱ and Ⅲ due to the amount of water flowing into reservoir decreased and pollutant load increased after 1997. Since 2000, the water quality has maintained at grade Ⅱ, and the quality is good enough to be satisfied with the standards of domestic use, industrial application, agricultural irrigation, aquaculture and landscape water standards. The water quality in Danghe reservoir belonged to grade Ⅰand Ⅱ, because people sparsely populate at the reservoir upstream and the sewage outfall of Dunhuang City is in the downstream of the reservoir. So the major type of pollution is non-point source pollution. The water quality in Chijinxia Reservoir is classified to trade Ⅴ because the sewage outfall of Yumen City is in upstream of the reservoir. So it is urgent to strengthen pollution abatement and control the pollution of point source in Shiyou river.