Soil organic carbon (SOC) is the most important indicators of soil quality and health. Identifying the spatial distribution of SOC and its influencing factors in cropland is crucial to understand the terrestrial carbon cycle and optimize agronomic management. Yunnan Province, characterized by mountainous topography and varied elevation, is one of the highest SOC regions in China. Yet its SOC stock of cropland and influencing factors has not been fully studied due to the lack of adequate soil investigation. In this study, the digital mapping of SOC at 1 km resolution and the estimation of total SOC stock in cropland of Yunnan Province was undertaken using 8637 topsoil (0–20 cm) samples and a series of spatial data through Random Forest (RF) model. It was showed that across the cropland of Yunnan Province, the mean SOC density and total stock were 4.84 kg m–2 and 337.5 Mt, respectively. The spatial distribution indicated that relatively high SOC density regions resided in the northwest and northeast parts of Yunnan Province. Elevation (19.5％), temperature (17.3％), rainfall (14.5％), and Topographic wetness index (9.9％) were the most important factors which controlled spatial variability of SOC density. Agronomic practices (e.g., crop straw treatments, fertilizer management) should be optimized for the sustainable development of crop production with high SOC sequestration capacity in Yunnan Province.