Waterlogging stress is a key driving force for the coordinated evolution of plants and environment in the hydro-fluctuation belt ecosystem of the ecological system in the Three Gorges Reservoir (TGR). Consequently, exploring the root traits of Salix variegata Franch., Salix babylonica L. under waterlogging stress and their impact on the soil environment have great significance for a comprehensive understanding of the adaptation mechanisms of willows under waterlogging stress. However, it is still uncertainty about the root characteristics of willows and their impact on the soil environment under the influence of off-season water level fluctuations in the TGR. We conducted a simulated flooding test (waterlogging, 2cm above the roots; control, no waterlogging) using the cuttings of S.variegata and S. babylonica in the TGR to reveal the effects of waterlogging stress on their root morphology, physiological characteristics, and rhizosphere soil enzyme activity. Results indicated that: compared with control, (1) the root surface area and root volume were increased significantly by 110.92% and 168.48% in two types of willows under waterlogging stress respectively. This indicated that the two types of willows respond to waterlogging stress by accelerating their root growth, enhancing the area and ability to absorb nutrients; (2) the CAT activity of two willow species was significantly decreased by 69.31% under waterlogging stress, while the POD and SOD activities did not show significant changes. This indicated that willows achieved a new dynamic equilibrium state by coordinating the stability of these three enzyme activities, thereby defending its ability to withstand waterlogging; (3) the SCAT and SSC activities in the rhizosphere soil were respectively increased in S. babylonica under waterlogging stress by 41.73% and 58.6%, while the urease activity in the rhizosphere soil of S.variegata was decreased by 47.89%. This indicated that there were interspecific differences in the impact of these two willow species on the soil environment, and S. babylonica has a better ability to enhance soil biological activity; (4) correlation analysis showed that root morphology was closely related to soil SCAT enzyme activity in two types of willows. Root SOD was positively correlated with rhizosphere soil SSC and SCAT activity, while root CAT was negatively correlated with soil SCAT, reflecting a close relationship between root morphology and rhizosphere soil microenvironment. In summary, the above results indicated that the root systems of two types of willows could effectively adjust their root morphology and physiological characteristics to adapt to waterlogging stress, and their root systems had certain improvement potential for the soil in the subsidence zone of the reservoir area. Moreover, the improvement of soil quality by the root system of S. babylonica was superior to that of S.variegata. The results of our study can provide a scientific reference for the application of willow trees in the ecological restoration of the TGR.