The pollution of Tarim River may have negative effects on ecosystem stability and sustainable de-velopment in the area of the middle and lower reaches. Using the actual measured data from Longkou and Shi daqiao observation stations on Aksu River and the Alar and 14 Tuan observation stations on the main stream of Tarim River in 2001-2005, authors carry out a research on water quality assessment of Tarim River based on the statistic software STATISTICA, principal component factor analyses, and water pollutant synthesis index methods. The result shows that water quality of the Longkou and Xidaqiao observation stations be-longs to first degree(cleanness) water, and the water quality of Alar and 14 Tuan observation stations be-longs to fourth degree(middle pollution) and fifth degree(serious pollution ) water, respectively. The major pollutants in Tarim River are chlorides, total hardness, mineralization degree, sulphate, fluoride, etc.