Lower reaches of Tarim River, Western China is a very serious arid and desertification region. During 2000-2006, 2.36 billion cubic meters water has been transported to this area by nine terms to control regional desertification. We apply grey correlation analysis for temporal and spatial variations of groundwater levels from nine monitoring sections and corresponding MODIS vegetation indices (VI) in the third, fourth, and seventh terms of water conveyance to evaluate the impacts of ecological water conveyances on basin hydrological processes and land cover. During the terms of water conveyance, both groundwater level and VI along the canal are rising and a calculated grey incidence degree reaches 0.9. However, the increases of groundwater levels and VI gradually reduce from the source of water input in the direction of the canal and calculated grey incidence degrees were below the level of significance for a single term of water conveyance. At same time, the incidence degrees reduced significantly with increasing distances from the canal. The analysis results shows that spatial variations of changes of hydrological processes and land cover conditions caused by water input were very large, which may reduce the use efficiency of precious water resource in this region.