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Understanding changes of soil organic carbon (SOC) in top layers of croplands and their driving factors is a vital prerequisite in decision-making for maintaining sustainable agriculture. However, high-precision estimation of SOC of croplands at regional scale is still an issue to be solved. Based on soil samples, synthetic image of bare soil and geographical data, this paper predicted SOC density of croplands using Random Forest model in the Black Soil Region of Jilin Province, China in 2005 and 2020, and analyzed its influencing factors. Results showed that random forest model that integrates bare soil composite images improve the accuracy and robustness of SOC density prediction. From 2005 to 2020, the total SOC storage in croplands decreased from 89.96 to 82.79 Tg C with an annual decrease of 0.48 Tg C yr−1. The mean value of SOC density of croplands decreased from 3.42 to 3.32 kg/m2, and high values are distributed in middle parts. Changes of SOC represented significant heterogeneity spatially. 62.14% of croplands with SOC density greater than 4.0 kg/m2 decreased significantly, and 38.60% of croplands with SOC density between 2.5 and 3.0 kg/m2 significantly increased. Climatic factors made great contributions to SOC density, however, their relative importance (RI) to SOC density decreased from 44.65% to 37.26% during the study period. Synthetic images of bare soil constituted 23.54% and 26.29% of RI in the SOC density prediction, respectively, and the contribution of each band was quite different. The RIs of topographic and vegetation factors were low but increased significantly from 2005 to 2020. This study can aid local land managers and governmental agencies in assessing carbon sequestration potential and carbon credits, thus contributing to the protection and sustainable use of black soils. [ABSTRACT FROM AUTHOR]