To investigate the effects of water level fluctuations on soil organic carbon in the drawdown zone of the Three Gorges Reservoir, samples of calcareous, purple and yellow soils were collected from areas subjected to different degrees of flooding. Statistical methods including Kruskal-Wallis non-parametric test and redundancy analysis were used for analysis. The results showed that periodic water inundation increased the organic carbon content and density of calcareous and purple soils, while decreasing the organic carbon content and density of yellow soils. Furthermore, the distribution of organic carbon in lime soil was influenced by aboveground biomass, pH and depth; organic carbon in purple soil was influenced by depth and aboveground biomass, whereas organic carbon content and density in yellow soil was associated with aboveground biomass, depth and belowground biomass. In summary, the effects of cyclic water level fluctuations on soil organic carbon in the drawdown zone were profound. However, the response of organic carbon to water level fluctuations varied between soil types. Future research will focus on elucidating the sources and stability mechanisms of soil organic carbon in the drawdown zone of reservoirs, providing essential support for ecological restoration and management in this region.