In order to study the variation of soil organic carbon in small watershed scale, the spatial variability of soil organic carbon contents in 0-10, 10-20, 20-40 cm was studied by geostatistical method. The results showed that the organic carbon contents in different soil layers in the watershed had a moderate intensity variation with strong spatial autocorrelation. The spatial variation of soil organic carbon content was obvious in the directions of 0 and 135°, and the spatial distribution was anisotropic. The results of Kriging interpolation showed that the contents of soil organic carbon in the shady slope were significantly higher than those in the sunny slope, and the contents of soil organic carbon in the high altitude area were higher than those in the low altitude area. Among the different soil layers, the contents of soil organic carbon were represented by Picea crassifolia > shrub > grassland, indicating that the different vegetation types had an important influence on the content and distribution of soil organic carbon. The spatial variability of soil organic carbon content was related to structural factors such as soil properties and topography factors, which provided a scientific basis for the measurement and description of soil information differences in the small watershed of Qilian Mountain.