Soil moisture content is one of the limiting factors for natural vegetation succession in alpine river valleys on the Tibetan Plateau. However, its spatio-temporal variability and effect on artificial vegetation restoration has rarely been reported. In this paper, we conducted a case study to examine the spatio-temporal variability and vertical characteristics of soil moisture by setting up a 100 x 120 m experimental plot on aeolian sandy land in a riparian ecotone and analyzing the result data using a geo-statistical approach. The soil moisture contents at different depths all showed strong temporal variability, with the mean soil moisture ranging from 4% to 6% in spring, from 6% to 14% in summer and from 9% to 12% in autumn. The Gaussian semi-variogram model was the best fitted theoretical model for the spatial structure of soil moisture contents in different seasons, and soil moisture at the field scale showed strong spatial dependence. The spatial patterns of soil moisture all demonstrated strong similarity between depths with the strongest between 0-20 cm and 20-40 cm depths in autumn. The soil moisture content over the upper 60 cm was the key factor that restricted the seed germination and seedling growth, and it affected vegetation coverage and density. The precipitation, variations of river water level, elevation as well as landform types were the main factors determining the variations of soil moisture content in different seasons. The results have important implications for the ongoing vegetation restoration in the study area.