The water-level fluctuation zone (WLFZ) of the Three Gorges Reservoir (TGR) experiences seasonal submergence and exposure, resulting in soil structure degradation and intensified erosion. This study investigated how flooding duration affects root development and the erosion resistance of root–soil complexes in the WLFZ of the TGR. Two representative herbaceous species were chosen for this study: Xanthium sibiricum, an annual with a taproot system, and Cynodon dactylon, a perennial with a fibrous root system. Root traits, soil erodibility K-value, shear strength, and soil texture were measured from plant and soil samples collected at different flooding durations (145–175 m elevations). Our results showed that prolonged flooding significantly suppressed root growth, particularly in the 145–155 m zone, where root length density and root tips were markedly reduced (p < 0.05). Soil erodibility increased with flooding duration, with erodibility K-values ranging from 0.050 ± 0.002 to 0.062 ± 0.001 t·hm²·h/(MJ·mm·hm²), while shear strength declined correspondingly. Textural shifts from silty loam to silt were observed at zones experiencing extended flooding, contributing to aggregate instability and decreased internal friction angles. Notably, Cynodon dactylon demonstrated superior soil reinforcement capacity compared to Xanthium sibiricum, with its root volume and surface area significantly correlated with reduced K-values (p < 0.01) and enhanced shear strength (p < 0.001), enabling it to better prevent bank erosion under flooding conditions. These findings underscore the importance of root morphological traits in maintaining soil stability under hydrological stress and highlight the potential of perennial fibrous-rooted species for vegetation-based erosion control in fine-textured riparian zones. This study provides a theoretical basis and practical reference for ecological restoration in the WLFZ of the TGR and similar environments.