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Water-level fluctuation (WLF) can destroy soil aggregates and induce soil organic carbon (SOC) loss, potentially triggering impacts on the concentration of atmospheric carbon dioxide. However, responses of soil aggregate content and aggregate-associated organic carbon to WLF have not been well studied, especially in the water-level fluctuation zone (WLFZ) of the Three Gorges Reservoir (TGR). Therefore, samples from different elevations (145 m, 155 m and 165 m) in the WLFZ of the TGR were collected for experiments. The wet sieving method was used to divide soil into silt and clay (<0.053 mm), micro-aggregate (0.053–0.25 mm) and macro-aggregate (>0.25 mm). The K₂Cr₂O₇-H₂SO₄ oxidation method was used to measure total SOC content in different soil aggregates. A modified Walkley and Black method was used to measure labile carbon in different soil aggregates. Results showed that macro-aggregate content substantially decreased, while micro-aggregate content remained stable and silt and clay fraction accumulated with a decrease in water-level elevations. Moreover, total SOC content and labile carbon in macro-aggregate were obviously higher than those in the micro-aggregate and the silt and clay fraction. Macro-aggregate contributed the most to SOC sequestration, while micro-aggregate contributed the least, and the contribution of macro-aggregate increased with a decrease in water-level elevations. We concluded that the macro-aggregate was the most active participant in the SOC sequestration process, and preferentially increasing the macro-aggregate content of the lowest water-level elevation was conducive to an improvement in soil carbon sequestration potential and would mitigate climate change. Full article