Based on 121 soil profile sample points in Ningxia, the spatial distribution characteristics of soil organic carbon (SOC) and the effects of climate, vegetation and soil factors on soil organic carbon at different depths (0-30 cm, 30-80 cm, 80-120 cm) were studied through correlation, variance partitioning analysis and structural equation modeling. Results showed that:(1) The SOC content presented a spatial distribution trend of lower in the middle and higher in the north and south at different soil depths in Ningxia. In 0-120 cm section, the SOC content decreased with the increase of soil depth, with an average value of 5.49 g/kg and a coefficient of variation of 90.71% indicating low SOC content and strong spatial heterogeneity. (2) Soil organic carbon in all soil layers was negatively correlated with mean annual temperature, drought index, calcium carbonate, pH, and positively correlated with mean annual precipitation, relative humidity, net primary productivity of vegetation, total nitrogen, total phosphorus, total potassium, calcium ion, cation exchange capacity, and clay content. (4) The action mode and degree of each factor on SOC in different soil layers were different. Soil total nitrogen, total phosphorus, calcium carbonate, and cation exchange capacity could directly affect soil organic carbon. The direct effect of mean annual temperature and net primary productivity of vegetation on soil organic carbon was not significant, and the indirect effect on soil organic carbon was mainly through soil properties. With the increase of soil depth, the effects of climate and vegetation were weakened, while the effects of soil were strengthened and became the main influencing factors. The results are helpful for the index screening of prediction and assessment of soil organic carbon content in Ningxia, and provide a theoretical basis for the relationship between regional ecosystem environmental factors and soil carbon cycle.