The Shennongjia Forestry District has been widely concerned with species diversity, with a large number of natural forests of rich species types and significant differences in vegetation types along the altitudinal gradient. This study focused on understanding the distribution characteristics of soil organic carbon content in natural secondary forests in the Shennongjia Forestry District. Using stepwise regression and structural equation modeling (SEM), we explored the multivariate relationships between soil organic carbon content and climate, elevation, soil properties, and stand structure. The soil organic carbon content was closely related to altitude, with significantly higher content at high altitudes compared to low altitudes. The average soil organic carbon content in the three altitudinal ranges was 27.37 g/kg (2000-2500 m), 21.56 g/kg (1600-2000 m), and 17.45 g/kg (1200-1600 m), respectively. The soil organic carbon content in the 0-20 cm, 20-40 cm, and 40-60 cm soil layers was 30.5 g/kg, 21.7 g/kg, and 13.73 g/kg, respectively. The contents decreased gradually with increasing soil depth, and there were significant differences among different soil layers (P < 0.05). Altitude, soil bulk, pH, and tree species diversity all showed a strong linear relationship with soil organic carbon content in all soil layers. Altitude indirectly affected soil organic carbon content by regulating soil bulk and pH, and this relationship remained consistent across all soil layers. The tree species diversity in the 20-40 cm and 40-60 cm soil layers indirectly contributed to soil organic carbon content by regulating soil bulk. The positive effect of tree species diversity on soil organic carbon content was strongly dependent on soil depth, especially in the deep soil layer (40-60 cm). Maintaining high tree species diversity can promote the carbon sink capacity of forest soils.