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Accurate assessment of soil C storage patterns and control factors on a regional and global scale is essential for predicting and mitigating soil C feedback to global environmental change. We used soil samples collected in the Shiyang River Basin in 2018, combined with remote sensing data, climate and meteorological data, watershed hydrological data, and soil physical and chemical properties to discuss the change characteristics and influencing factors of soil organic carbon (SOC) under different soil depths in the Shiyang River Basin in an arid area and analyze the storage model and carbon sequestration potential of soil organic carbon in different geomorphic units. The research results show that, (1) in spatial distribution, the SOC content in the Shiyang River Basin shows an obvious regional difference, and the average content of SOC in the oasis area in the middle reaches significantly higher than that in the mountain area in the upstream and desert area in the downstream. In vertical distribution, the content of SOC in the whole watershed decreases with the soil depth increase. (2) Soil carbon sequestration potential decreased with the increase in soil depth, but there were regional differences. The Oasis area in the middle reaches of the Shiyang River Basin is a high-potential area. In contrast, most of the upper mountain areas and the lower reaches of the desert area are low-potential areas. Environmental factors such as vegetation cover, meteorological factors, and physical and chemical properties of soil are important factors that promote the spatial variability of SOC content. The decisive effect of environmental factors on the SOC content is most significant in the surface layer 0–20 cm. [ABSTRACT FROM AUTHOR]