Abstract: Background Soil structure stability reflects soil's ability to resist water erosion, which is closely related to the content of soil water-stable aggregates and their organic carbon content, and largely determines the intensity of soil erosion. Thus, unraveling the distribution characteristics of organic carbon in soil aggregates and differences in structural stability under the background of land use change is critical for providing theoretical basis for soil erosion prevention and organic carbon sequestration mechanisms analyzing. Nevertheless, knowledge regarding the response of soil structure stability to the content of soil water-stable aggregates and their organic carbon content was still unclear in the Three Gorges Reservoir Area (TGRA). Methods To investigate the distribution characteristics of soil aggregate organic carbon and its effects on soil structural stability under different land use types in the purple soil region of the TGRA, six typical land use types within the Huangdunxi small watershed in Jiangjin District were selected. Vegetation characteristics and soil properties, water-stable aggregates content of different particle sizes and their organic carbon contents were measured, then soil structural stability parameters (soil structural stability index, SSI; mean weight diameter, MWD; geometric mean diameter, GMD) were calculated. Differences in water-stable aggregates of different particle size classes and their organic carbon content, as well as soil structural stability, under various land use patterns were analyzed, the dominant influencing factors attributed to these differences in soil structural stability were identified. ResultsThe results showed that soil aggregates and organic carbon contents, and structural stability differed significantly among different land use types. Except for sloping farmland, particle sizes of water-stable aggregates for other five land use types were dominated by >0.25 mm aggregates content , but the content of 5–2 mm aggregate was the minimum in all land use types. The organic carbon content among different water-stable aggregates sizes exhibited a unimodal distribution, it initially increased and then decreased with the increase of aggregate size, and organic carbon content of <0.25 mm aggregate was the minimum. The SSI values ranked as evergreen coniferous forest > evergreen broad-leaved forest > shrubland > grassland > economic forest > sloping farmland. Moreover, MWD and GMD ranked as shrubland > evergreen coniferous forest > evergreen broad-leaved forest > grassland > economic forest > sloping farmland, soil structural stability of sloping farmland was the worst, then followed by economic forest. Redundancy analysis revealed that soil organic carbon, >5 mm aggregates, silt, 5-2 mm aggregate organic carbon, 2-0.25 mm aggregates, and <0.25 mm aggregate contents were the primary factors attributed to the differences in soil structural stability, of which explaining 98.03% of the variations. Among these factors, soil organic carbon and >5 mm aggregate content were the dominant influencing factors, accounting for 56.11% and 17.28% of the variations, respectively. Conclusions In conclusion, orchards and sloping farmland remain potential sources of soil erosion in the Three Gorges Reservoir Area. Given the rapid growth trend of orchards along the river in recent years, improving soil structure and enhancing erosion resistance in these orchards are crucial for controlling soil erosion and non-point source pollution loss in the reservoir area, which is vital for achieving green development in the Yangtze River Economic Belt.