Abstract: Climate change has significantly perturbed atmospheric circulation patterns, precipitation regimes, and the frequency of extreme temperatures, thereby exacerbating the occurrence of severe natural disasters. Focusing on the middle reaches of the Yangtze River Basin, this study integrates five General Circulation Models (GCMs) from the Coupled Model Intercomparison Project Phase 6 (CMIP6) with the Soil and Water Assessment Tool (SWAT). The HEC-RAS model was subsequently employed to project the maximum inundation extent and the evolution of spatial flood risk patterns under three Shared Socioeconomic Pathways (SSPs: SSP1-2.6, SSP3-7.0, and SSP5-8.5) across the near-future (2031–2060) and far-future (2061–2090). Results indicate that future extreme precipitation will substantially amplify regional inundation risks. By the end of the 21st century (2061–2090), the maximum inundated area is projected to increase by 0.85%–9.39%, 0.50%–9.57%, and 0.68%–9.42% under SSP1-2.6, SSP3-7.0, and SSP5-8.5 scenarios, respectively, relative to the baseline period (1995–2014). Furthermore, the mainstream reach from Yichang to Zhicheng exhibits a progressive flooding regime characterized by "channel storage, floodplain overflow, and hinterland inundation." This research advances the understanding of the long-term evolutionary dynamics of flood events under climate change and elucidates the modulating effects of hydraulic engineering operations on flood processes. The findings provide critical insights for integrated river basin management, disaster risk reduction strategies, and evidence-based scientific decision-making.