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Changes in soil organic matter (SOM) can affect food security, soil and water conservation, and climate change. However, the drivers of changes in SOM in paddy soils of China are not fully understood because the effects of agricultural management and environmental factors are studied separately. Soil, climate, terrain, and agricultural management data from 6 counties selected based on representative soil types and cropping systems in China were used in correlation analysis, analysis of variance, and cforest modeling to analyze the drivers of changes in SOM in paddy soils in the Middle and Lower Yangtze River Plain from 1980 to 2011. The aims of this study were to identify the main factors driving the changes in SOM and to quantitatively evaluate their individual impacts. Results showed that the paddy SOM stock in the study area increased by 12.5% at an average rate of 0.023 kg m−2 year−1 over the 31-year study period. As a result of long-term rice planting, agricultural management practices had a greater influence than soil properties, climate, and terrain. Among the major drivers, straw incorporation, the most influential driver, together with fertilization and tillage practices, significantly increased the accumulation of SOM, while an increase in temperature significantly influenced SOM decomposition. Therefore, to confront the challenge of rising temperatures, it is important to strengthen the positive effects of agricultural management. Rational fertilizer use for stabilizing grain production and crop straw incorporation are promising measures for potential carbon sequestration in this region.