In order to explore the effect of water level fluctuation on soil organic carbon in the hydro-fluctuation belt of the Three Gorges Reservoir, lime soil, purple soil and yellow soil samples and their plant samples affected by different flooding intensities were collected and tested, and Kruskal-Wallis non-parametric test and canonical analysis based on redundancy analysis were used for investigation. The results showed that periodic flooding increased the organic carbon contents and densities of calcareous soil and purple soil, but decreased the organic carbon content and density of yellow soil. In addition, the distribution of organic carbon in calcareous soil was also affected by aboveground biomass, soil pH and soil depth. The organic carbon in purple soil was also affected by soil depth and aboveground biomass, while the organic carbon content and density in yellow soil were related to aboveground biomass, soil depth and underground biomass. In short, periodic water level fluctuations have a profound impact on soil organic carbon in the hydro-fluctuation belt, but soil types differentiate the response of organic carbon to water level fluctuations.