Soil moisture plays a crucial role in the hydrological cycle and climate system. The reliable estimation of soil moisture in space and time is important to monitor and even predict hydrological and meteorological disasters. Here we studied the spatiotemporal variations of soil moisture and explored the effects of precipitation and temperature on soil moisture in different land cover types within the Tarim River Basin from 2001 to 2015, based on high-spatial-resolution soil moisture data downscaled from the European Space Agency’s (ESA) Climate Change Initiative (CCI) soil moisture data. The results show that the spatial average soil moisture increased slightly from 2001 to 2015, and the soil moisture variation in summer contributed most to regional soil moisture change. For the land cover, the highest soil moisture occurred in the forest and the lowest value was found in bare land, and soil moisture showed significant increasing trends in grassland and bare land during 2001~2015. Both partial correlation analysis and multiple linear regression analysis demonstrate that in the study area precipitation had positive effects on soil moisture, while temperature had negative effects, and precipitation made greater contributions to soil moisture variations than temperature. The results of this study can be used for decision making for water management and allocation.