[Objective] The karst and non-karst areas in Southwest China are interlaced with strong spatial heterogeneity. Assessing the spatial differentiation and storage of soil organic carbon (SOC) in this region at the county scale is of great significance for achieving regional "dual carbon" goals. [Methods] Taking Wenshan County, a typical karst county in southeast Yunnan Province, as an example, we employed a grid sampling method to conduct the spatial differences in SOC content and storage in top soil(0-20 cm) and deep soil(0-200 cm). Furthermore, we used the semi-variogram function and geographical detector to analyze the impact of external environmental factors on the spatial differentiation of SOC. [Results] The average SOC content in the top soil and deep soil was 17.80 g/kg and 5.18 g/kg respectively, with a total storage of 3770.89×104 t. The distribution pattern revealed higher SOC content in the topsoil of the western region and lower in the central and northern regions, while the deep soil exhibits higher SOC content in the central and western regions and lower in the northeastern region in Wenshan County. In non-karst areas, the SOC content in the topsoil and deep soil was 20.88 g/kg and 6.12 g/kg, respectively, which was 27.94% and 32.75% higher (P<0.01) than in karst areas. The semi-variogram model indicates that the nugget effect value of SOC ranges from 14.62% to 59.93%, indicating that structural factors dominate the spatial differentiation of SOC in Wenshan County. According to the analysis of the geographical detector, temperature and altitude are the main controlling factors affecting SOC in the top soil layer in karst areas. As the temperature decreases and the altitude increases, the SOC content in Wenshan County shows an increasing trend. However, the SOC content in karst areas is generally lower than that in non-karst areas due to their lower altitudes, severe rocky desertification, and relatively poor vegetation growth. For the deep soil, precipitation is the main controlling factor affecting SOC in karst areas. The leaching effect caused by precipitation may combine dissolved calcium with organic matter to form humic acid calcium, promoting the accumulation of SOC in deep soil. In non-karst areas, stratigraphic chronology plays a leading role. The soil developed from Permian basalt parent material may have higher soil clay and macro-aggregate contents, which helps to maintain the physical protection and stability of SOC in deep soil. [Conclusion] This study will provide a reference for the precise assessment of SOC and the regulation of soil carbon pools in the southwestern karst region.