Abstract: Based on the GIS, and the statistical data of cities and counties of Xinjiang, this paper analyzed the characters of land use change and its eco-effects in southern Xinjiang. The results showed that: 1) In 1996-2008, arable land, garden, forest, water area and construction land have increased, however, the grass land and unused land area decreased. The dynamical degree of land use was 0.88%, garden, construction land and arable land showed bigger annual change rates; forest, grass land, water area and unused area showed smaller annual change rates. There was an obvious regional difference in land use change. Except the unused land area, the other types of land use changes in Bazhou were bigger than the same types land use changes in whole Southern Xinjiang, while the all types of land use changes in Hotan were smaller than the same types land use changes. 2) With the increase of population, human activities changed land use structures, enlarged oasis arable land area, which brought destructions to the desert vegetation. The bad ecological effects were as follows: desertification, land solemnization, land barrenization, arable land pollution, reducing of grassland, ecological deterioration of plain reservoir and ecological degradation of ecotone between oasis and desert, as a result, the sustainable development of oasis was affected seriously by these effects.