Spatiotemporal variability in soil organic carbon (SOC) plays key roles in ecosystem stability and terrestrial carbon cycling. However, the inter-decadal characteristics of SOC variability and its climate drivers in China from the 1980s to 2010s remain unclear. In this study, a modeling framework for combining spatiotemporal prediction models was proposed. Within this model, soil samples from each of the two periods were combined and calibrated to obtain three models, and their prediction outputs were selectively combined to obtain SOC maps for the different inter-decadal periods. A total of 8473 soil samples from three periods (1980s, 2000s and 2010s) were used for model validation. The results suggested that the SOC prediction accuracy in the top 0–20 cm of soil (SOC020) was better than that of the first meter of soil (SOC0100), and the predicted spatial patterns shared characteristics with findings from previous studies. Predictions for the 1990s exhibited relatively high uncertainty, especially in the Tibetan Plateau, Tien Shan, and Northeast China. Both individual and coupled climatic factors exerted scale- and location-specific effects on the SOC. Coupled climatic factors accounted for more than 65% of the SOC variability in both soil layers. The regional SOC in North and Northeast China exhibited inter-decadal decline. Soil in China functioned as carbon sinks from the 1980s to 2010s at a national scale, with SOC020 increasing from 30.40 Pg to 33.97 Pg and SOC0100 from 79.29 Pg to 82.26 Pg. Overall, our results provide reliable baseline data for optimizing carbon cycle models of terrestrial ecosystems, and to guide future carbon sequestration policies.