<p>Paddy soil serves as a significant reservoir of soil organic carbon (SOC) and a source of agricultural greenhouse gases (GHGs), and its long-term flooded conditions can influence SOC turnover by affecting a range of geochemical processes. However, the key processes and mechanisms controlling the turnover of SOC fractions in paddy soil remain elusive. Here, we conducted a 40-day anoxic microcosmic culturation of paddy soil, and assessed the transformation of SOC fractions alongside Fe, N, and S species. A comprehensive analysis was conducted by integrating chemical analysis, advanced characterization and modeling methods. Results indicated an increase in CH₄, CO₂ and chronic SOC pool content, accompanied by a decline in the active and inert SOC pools. The SOC turnover was mainly through the release process in the first 20 days and driven by microbial decomposition in the&#xa0;last 20 days, while the reduction and dissolution of iron minerals was a key factor. <i>Clostridium</i> and <i>Fonticella</i> became the dominant genera in the later stage of flooding, and they were related to iron cycling and methane production, respectively. Our model results revealed that the reaction rates of transformation from the inert SOC pool to the active SOC pool were faster, and the active SOC fraction was then rapidly decomposed and mineralized into CH₄ and CO₂. Although the decrease (13.98% of total SOC) in the inert SOC pool was comparable to the increase (14.36% of total SOC) in chronic SOC pool, the accumulation was attributed to its inherent molecular persistence. These findings are important for the evaluation and prediction of SOC behaviors in flooded paddy soils.</p> Graphical Abstract <p></p>