Abstract: Geotextile mattresses are widely adopted in waterway regulation projects in the middle and lower reaches of the Yangtze River due to their favorable riverbed protection performance and outstanding scour resistance against fluvial disturbances, serving as a core protective measure for stabilizing riverbed and ensuring waterway navigability. After the impoundment of the Three Gorges Reservoir in 2003, the whole hydrosedimentological environment of waterway regulation projects distributed downstream of the dam has undergone dramatic and irreversible changes, and a series of previously unobserved new damage characteristics of the geotextile mattress structure have gradually emerged under long-term operating conditions of clear-water discharge with drastically reduced sediment supply, posing serious risks to the safe and stable operation of waterway regulation projects and even threatening the normal navigation of the waterway. Taking the geotextile mattress anti-scour revetment project on the right side of Liutiaozhou in the main stem of the Yangtze River as a representative field case, this work analyzes the typical damage patterns and failure processes of soft mattresses, identifies the dominant factors controlling structural damage by integrating hydrological, topographic and material-related factors, and elaborates the multi-scale damage evolution mechanism of geotextile mattresses under the coupled effects of persistent riverbed scouring and seasonal dry-wet alternation based on long-term field measurements such as annual hydrological regime variation and high-precision riverbed topography monitoring records collected over more than ten years. The results show that structural failure of geotextile mattresses results from the synergistic interaction of multiple interrelated factors, including complex near-bank hydrodynamic conditions, altered flow-sediment regimes, inherent riverbed boundary constraints, and inherent mechanical properties of geotextile mattress materials. The revetment along the right margin of Liutiaozhou is subject to persistent strong scouring by high-speed near-bank flow all year round. After the impoundment of the Three Gorges Reservoir, the thalweg adjacent to the right margin of Liutiaozhou shifted markedly leftward, further intensifying the scouring intensity within the entire revetment zone and aggravating local scour damage to geotextile mattresses. Meanwhile, sediment transport downstream of the reservoir has dropped sharply since the impoundment of the Three Gorges Reservoir, which intensifies continuous riverbed erosion at the foot of the Liutiaozhou revetment. Scour-induced sediment loss at the peripheral edges of geotextile mattresses deprives the mattress structures of uniform effective structural support and further exacerbates their deformation and failure severity. In addition, the low-water level downstream of the reservoir has kept declining year by year after reservoir impoundment. The geotextile mattress, which was barely exposed above the water surface previously, now shows markedly longer exposure durations. Geotextile mattresses are fully exposed to intense solar radiation and atmospheric weathering during dry seasons and become fully saturated and swell significantly in flood seasons. Long-term wetting–drying cycles repeatedly damage the microstructures of mattress geosynthetic materials, resulting in continuous degradation of mechanical properties and long-term durability, and thus significantly accelerating the structural failure of geotextile mattresses. This study verifies the previous finding that hydrodynamic action and riverbed scouring are important influencing factors for geotextile mattress damage and identifies two previously overlooked key factors, namely the sustained decline in downstream water levels and repeated wetting–drying cycles following the impoundment of the Three Gorges Reservoir, thereby improving the systematic understanding of geotextile mattress damage mechanisms under the typical clear-water discharge environment of large cascade reservoirs. The research results can provide important theoretical support and practical technical reference for the structural design, parameter optimization and long-term engineering operation and maintenance of geotextile mattress structures in the middle and lower Yangtze River and other similar alluvial river sections with analogous hydrosedimentological conditions, and also offer valuable analytical insights into effective disaster prevention and risk control for river regulation projects.