【Objective】Mineral-associated organic carbon (MAOC) is a key component of the stable organic carbon pool in soils. Its saturation status directly determines the soil carbon sequestration potential and is therefore crucial for assessing soil carbon storage capacity and formulating climate change mitigation strategies. Due to the unique hydrological regime of the Three Gorges Reservoir, soil in the riparian zone of the Three Gorges Reservoir has been experienced periodic flooding stress for a long time. This special environment might have a profound influence on the composition of clay minerals and its capacity to stabilize organic carbon. However, it remains unclear how flooding stress drives changes in clay minerals and how these changes further influence the saturation of organic carbon. 【Method】To address this gap, this study first systematically analyzed the composition and content of clay minerals in the 0-30 cm soil layer across different elevation zones in the riparian area of the Three Gorges Reservoir. Second, using the Hassink empirical model, we estimated the organic carbon saturation capacity (CSC) and organic carbon sequestration potential (CSP) of these soils. Finally, we quantitatively assessed how various clay minerals regulate the saturation degree of soil organic carbon. 【Result】The results show that the illite-smectite mixed-layer minerals and chlorite-smectite mixed-layer minerals are the main clay minerals in the riparian zone of the Three Gorges Reservoir, accounting for 44.52% and 30.38% of the total clay minerals, respectively. Flooding stress altered the clay mineral composition: as the intensity of flooding increased, the content of illite-smectite mixed-layer minerals decreased, while the proportions of illite, kaolinite, and chlorite increased. In addition, flooding stress has a significant effect on soil organic carbon saturation in the riparian zone. In Wushan and Yunyang, CSC showed a V-shaped distribution trend, while in Fuling, it showed the opposite change. At the same time, the unit-area CSP and regional CSP were weakened by strong flooding stress. The RCSP at the 165-175 m elevation was about 1.94 times greater than that at the 145-155 m elevation. The results of random forest analysis and correlation analysis show that the CSP in the riparian zone has a significant negative correlation with illite, kaolinite, and chlorite, and a significant positive correlation with the illite-smectite mixed-layer minerals, which are the main clay minerals affecting CSP. It is worth noting that the correlation between CSC and clay minerals changes significantly at different water level elevations, and with the enhancement of flooding stress, this correlation gradually weakens and the correlation direction changes. 【Conclusion】This study reveals the complex impacts of flooding stress on clay mineral composition and its influence on the saturation of mineral-associated organic carbon in the riparian zone. These findings provide theoretical support for understanding soil carbon cycling mechanisms and enhancing soil carbon sequestration potential in riparian zones.