Soil moisture is the main driving force for the patterns and processes in arid and semi-arid ecosystem, and topography-vegetation factors are the main factors affecting soil moisture on the small-scale. Soil moisture at different depths (0-40 cm in surface layer, 40-200 cm in middle layer, 200-300 cm in deep layer and 0-300 cm in whole) on fixed sand dunes near the northern sand dune in the southern edge of the Gurbantunggut Desert was used as a study object to investigate the relationship and variation patterns between soil moisture and topography-vegetation factors using generalized linear model (GLM), generalized additive model (GAM) and random forest (RF) models. The results showed that: (1) Soil moisture at different depths showed a consistent single-peaked distribution, and the magnitude of soil moisture at different depths was in the order of: deep > middle > surface, and there were significant differences between the two. (2) The vegetation and terrain factors affecting soil moisture at different depths obtained by GLM and GAM models were identical, and the accuracy of the RF model was better than that of GLM and GAM models. (3) Topographic factors elevation, slope, height difference and vegetation factors shrub multiplicity were negatively correlated with soil moisture at different depths under their influence, while topographic factors slope direction (specified as 0 due east, rotated clockwise) and vegetation factor biomass were positively correlated with the soil moisture they affected. The vegetation factor herbaceous cover was positively correlated with surface soil moisture and negatively correlated with mesocosm soil moisture. The results of the study can provide theoretical reference for the formulation of corresponding wind and sand control measures and the establishment of scientific and reasonable vegetation sand fixation model in the study area.