In order to investigate the vertical distribution characteristics of Soil Organic Carbon (SOC) under different Biological Soil Crust (BSC) types in the Gurbantunggut Desert and analyze their influencing factors, this study focused on three different ground cover types: Moss, Cyanobacterial, and Bare Sand. Field samples of different BSC types and the underlying 0-2 cm, 2-5 cm, 5-10 cm, 10-20 cm, 20-30 cm, 30-50 cm, 50-70 cm, and 70-100 cm soil layers (Bare Sand control) were collected. The SOC content and soil physicochemical properties in different soil layers were measured for further analysis. The results revealed that: (1) The SOC content in the 0-100 cm soil layers generally decreased with the increasing soil depth across different ground cover types. However, there was an increase of SOC content in the 10-30 cm soil layer. The SOC content ranged from 1.61 to 2.70 g/kg in Moss, 1.41 to 2.56 g/kg in Cyanobacterial, and 1.21 to 1.92 g/kg in Bare Sand. (2) The significant differences in SOC content were observed among different ground cover types in the 0-5 cm soil layer, while there were no significant differences for SOC content in the 5-100 cm soil layers. SOC content within the same layer followed the order: Moss>Cyanobacterial>Bare Sand control. (3) Pearson correlation analysis indicated that SOC content was positively correlated with nutrients (total nitrogen and total phosphorus) and negatively correlated with pH and electrical conductivity (EC) under different ground cover types. Structural Equation Modeling (SEM) results demonstrated that soil nutrients and particle size (percentage of sand) were main factors affecting the vertical distribution of SOC. Particle size was the primary influencing factor for Bare Sand and Cyanobacterial, while nutrients (total phosphorus) played more significant role in Moss BSC. The development of BSC gradually enhanced the accumulation of soil carbon, altered the vertical distribution characteristics of organic carbon, and had the most pronounced impact on SOC in soil layers above 5 cm. It played a regulatory role in the vertical distribution characteristics in conjunction with soil physicochemical properties.