In order to determine the effects of land-use types and dam-triggered flooding intensity on soil active organic carbon fractions and identify the main influencing factor in the riparian zone of the Three Gorges Reservoir, soils from different flood intensities and land-use types were collected as study objects and were used to quantitatively analyze soil active organic carbon fractions, while the relationships between soil active organic carbon fractions and soil physical and chemical properties were analyzed. The results showed that the content of soil active organic carbon decreased with the increase of flooding intensity. The land-use types, flooding intensity, and their interaction explained by 22.1%, 13.7%, and 9.3% respectively, on soil organic carbon variation. Soil microbial biomass carbon was mainly affected by land-use types and the interaction between land-use types and flooding intensity, and their variation partitioning for the effects on soil microbial biomass carbon were 3.9% and 0.6%, respectively. Soil dissolved organic carbon and soil particulate organic carbon were mainly affected by the dam-triggered flooding intensity, and the explanations for their variation partitioning were 65.1% and 5.5%, respectively. Multiple factor analysis showed that significant correlations between the MBC content of soil active organic carbon and soil electrical. However, Water flooding intensity might affect TN and C:N in soil properties, and further affect the distribution of DOC. Soil POC content was significantly positively correlated with SOC content, and POC can be used as an indicator to measure the flooding intensity changes of organic carbon pool in the riparian zone of the Three Gorges Reservoir.