Soil structure stability is crucial for evaluating the restoration and maintenance of degraded ecosystem functions. Plant growth has been found to exert various influences on the evolution of soil structure, through both direct and indirect mechanisms. Understanding how different configurations of dominant plant species impact soil structure stability is essential for optimizing restoration strategies in degraded ecosystems. This is particularly important in regions prone to erosion and habitat degradation, such as the riparian zones of large reservoirs. We selected three dominant plant species from the riparian zone of the Three Gorges Reservoir: Cynodon dactylon (G), Cyperus rotundus (X), and Xanthium sibiricum (C). Three treatment groups were implemented: control (CK), single species (G, X, C), and two-species mixtures (GX, CX, CG). Soil aggregates were assessed using Yoder's wet sieving method, and soil pore characteristics were examined through computed tomography (CT). The aim was to compare the effects of different plant configurations on the size distribution and stability of soil aggregates and soil pore structure. The results showed that: 1) The mass percentage of soil aggregates larger than 0.25 mm increased under all plant configurations treatments compared to the CK treatment. Plant root growth facilitated the formation and stabilization of soil aggregates, although the effect was not statistically significant. 2) Cyperus rotundus, whether planted alone or in mixture with Cynodon dactylon, inhibited the formation of soil macropores. This was likely due to its underdeveloped root system and the compressive effect of its enlarged root nodules on the surrounding soil pores during growth. In contrast, Cynodon dactylon and Xanthium sibiricum, either planted individually or in mixtures, consistently promoted the development of soil macropores. 3) Plant root traits exhibited significant correlations with both soil aggregate stability and soil pore structure. Root length (RL) and root surface area (RSA) were identified as the primary traits influencing soil aggregate stability, while root length (RL), root surface area (RSA) and root volume (RV) were found to be critical in controlling soil pore structure. To effectively enhance soil structural stability, plants can be selected based on root traits such as root length and surface area to identify pioneer or dominant species suitable for vegetation restoration in fragile ecosystems. This study provides essential data and theoretical insights for optimizing plant species selection and community design to enhance soil and water conservation, as well as ecological restoration in the riparian zones of the Three Gorges Reservoir and other similar environments prone to degradation.