Spatial variation of soil moisture after snow thawing in South Gurbantunggut was quantitatively studied using ANOVA and geostatistics at various scales. The results show that the soil moisture heterogeneity varies along with spatial scales. At the shrub individual scale, there is a gradient in soil moisture from shrub-canopied area to canopy margin and to the interspaces between shrubs. At the community scale, soil moisture is highly autocorrelated and the semivariogram is fitted as spherical model, with an 89.6% structural variance and a range of 4.02 m. In addition, Kringing map indicates that the soil moisture distribution pattern after snow thawing is highly consistent with the shrub patch pattern. At the typical inter-dune transect scale, soil moisture presents a pattern of high value at inter-dune depression and low value at dune, and this variation is fitted as Gaussian model with a structural variance of 95.8% and a range of 66.16 m. The range is comparable with the scale of topography zoning, suggesting that the topography pattern controls the pattern of snowmelt at this scale. The evidence indicates that the heterogeneity of soil moisture at various scales is controlled by various land surface processes after snow thawing. For Gurbantunggut Desert, the spatial heterogeneity of snowmelt at various scales is ecologically valuable, because it promotes the utilization efficiency of the snowmelt for the desert vegetation.