The water level fluctuation zone (WLFZ) of the Three Gorges Reservoir (TGR) represents a unique ecotone shaped by reversed hydrological rhythms that significantly influence plant dynamics and soil organic carbon (SOC) processes. However, the contribution of plants to SOC storage after the establishment of stable plant communities remains unclear. A field investigation and soil sampling were conducted in the WLFZ of the TGR in 2023, covering both the main stream and tributary regions in middle- (155-165 m) and high-elevation (165-175 m) zones. The plant composition, diversity, and carbon and nitrogen contents of soil and vegetation and the carbon stable isotope ratio signatures were analyzed. Results showed that plant diversity increased with elevation, while biomass allocation varied significantly between elevation zones. Cynodon dactylon (L.) Pers. had a significantly higher biomass than Xanthium strumarium L., both of which were identified as dominant species in the WLFZ based on their high importance values. The response of SOC storage to elevation differed between regions: in the main stream, SOC storage was 23% higher in the middle-elevation than in the high-elevation zone, while in the tributary, SOC storage in the high-elevation zone exceeding that in the middle-elevation zone by 38%. Soil total nitrogen and the C/N ratio were the primary factors controlling SOC storage, explaining 68.6% of the variance, while plant effects were relatively weak. Isotopic mixing model results indicated that X. strumarium contributed 34.84% to SOC storage at 165-175m, whereas C. dactylon contributed 21.06% at 155-165 m, but this difference occurred within the context of a minor overall plant contribution to SOC. These results highlight that SOC dynamics are primarily controlled by soil factors (soil nitrogen and the C/N ratio), with plants having a secondary effect.