The change in soil organic carbon fraction in wetland ecosystem plays an important role in global climate change. The objective of this study was to determine the change in organic carbon and its fractions at different elevation gradient in riparian wetland of Three Gorges Reservoir Area. Results showed that soil organic carbon(OC), readily oxidizable carbon(ROC), water-soluble carbohydrates(WSCh), water-soluble organic carbon(DOC) and microbial biomass carbon(MBC) were lower in the riparian wetland than these in the never inundation upland. In riparian zone, the soil OC, ROC and MBC in sites with lower elevation gradient, longer-term inundation and fluctuating were lower than these in other sites, while soil mineralized carbon (MIC) changed oppositely. The positive correlation of MBC with OC (R~2=0.94) was significantly higher than that with ROC, DOC and WSCh (R~2=0.88,0.73 and 0.70),whereas there was no significant correlation between OC and MIC. These results suggested that MBC was the fraction of soil organic carbon which was the most sensitive to change of elevation gradient in riparian wetland of Three Gorges Reservoir Area.