The Cherchen River is a unique tributary of the Tarim River. The river directly supplies to the common terminal lake, an endorheic lake, not to the main stream of the Tarim River. The Tetima Endorheic Lake is the most important lake in southeastern Tarim Basin, but it had dried up from 1972 to 2002. Fortunately, in 2000, an Emergency Ecological Water Transfusion (EEWT) project initiated in the lower reaches of the Tarim River by Xinjiang Tarim River Basin Management Bureau. As one of many good results, Tetima Lake has refilled since 2002. In recent years, there is several research projects carried out in the lower reaches of the Tarim River to assess the effect of EEWT in different fields, such as lake area, water quality, ground water table, vegetation vitality, seed bank, biodiversity, micro climate, etc. Some research showed that water area in Tetima-Kanglayka lake region is increasing, and the main driving force of this change (EEWT project) is summarized. In this research using vegetation index and water index as determining parameters of decision tree, the land cover information, include various forms of water areas in the entire watershed of the Cherchen River sub-basin, was extracted by using Landsat Images in 1990, 2000 and 2010. Land cover changes were analyzed based on the classification system established based on 3rd level of FAO/UNEP Land Cover Classification System. It is revealed that water area changing speed in the period of 2000-2010 was faster than that in the period of 1990-2000, especially in lakes, of which area and number were increasing comparatively. Among various water bodies, glaciers and snow covers shrunk significantly. The area of glaciers and snow covers, distributed in the areas lower than 5 000 m, were account for 38.8% of all glaciers and snow covers in the entire watershed in 1990, but in 2010, it reduced to 5.4%. The area and number of rivers had changed not so much, but the area and number of lakes had increased greatly. The lakes area in 2010 was 5 times more than that in 1990, and most of new-formed lakes were distributed in the plain areas in the lower reaches. As a result of climate change and water body change, natural vegetated lands are expanding continuously both in the mountain areas and plain lands, especially those at high altitude, except for deserts (including all kinds of non-vegetated, non-water covered lands and also non-artificial lands), which are decreasing. The vegetated lands in the mountain areas are expanding faster than those in plain; accordingly, the shrinking speed of deserts in the mountains faster than that in the plain areas. Through correlation analysis, it is found that the influence of natural factors is greater than that of human factors in the whole Cherchen River watershed in the period from 1990 to 2010.