Using the methods of coefficient of variation (CV）, Pearson correlation and regression analysis, the paper analyzed the spatio-temporal variation of soil moisture, the distribution of vegetation and the relationship between them for the period 2002-2006 in the lower reaches of Tarim River. Results showed that in spatial the soil moisture of horizontal direction decreased with the distance away from water source, and that of vertical direction increased with the soil depth increasing. The soil moisture in the 0-60 cm layer had the least CV belonging to moderate variability, and that below 60 cm had the larger CV belonging to strong variability. In temporal the variability of soil moisture was restricted by both the amount and the duration of ecological water delivery. The spatio-temporal distribution of soil moisture was synchronized with that of vegetation in this area. The characteristic index of vegetation was significantly correlated to the soil moisture in the layer 80-280 cm; Meanwhile both of them had the negative correlation with (the groundwater depth significantly. It indicated that the soil moisture in the soil layer blow 60cm (affected the growth and distribution of vegetation significantly, and that groundwater table was the leading factor that determined the spatio-temporal variability of soil moisture and vegetation.