Abstract: The functional restoration of large river ecosystems represents a significant global challenge. The “Ten-Year Fishing Ban” implemented across the Yangtze River Basin, a large-scale ecological intervention, offers an unprecedented opportunity to investigate the recovery processes in a highly regulated aquatic ecosystem. This study aimed to comprehensively explore structural changes in the fish community food web in the tailrace of the Three Gorges Reservoir (TGR) after the fishing ban. We focused on two hydro-morphologically distinct river sections, the downstream Fuling section and the upstream Mudong section, to analyze the spatio-temporal responses of the food web. Our methodology integrated stable isotope analysis (δ¹³C and δ¹⁵N), an advanced Bayesian Isotope Mixing Model (BIMM) incorporating trophic-level constraints and prior dietary information, and food web topological analysis. Fish and basal food source samples were collected before (2018—2019) and after (2023) the ban implementation. Our results reveal that although species richness recovered similarly in both sections (increasing to 36species each), food web restructuring followed two divergent pathways shaped by local habitat . The food web exhibited “vertical deepening”: connectance decreased from 0.085 to 0.070 and generalization index from 2.55 to 2.44, indicating more specialized trophic interactions. Concurrently, an expanded δ¹⁵N range (10.94‰ to 11.51‰) reflected food chain elongation, and the propo rtion of omnivorous species rose from 58.3% to 65.5%. These shifts, together with an increased piscivorous diet in the key predator Siniperca kneri, support a top-down recovery cascade driven by restored predator populations. In contrast, the riverine Mudong section underwent “bottom-up reorganization” toward a flatter structure: connectance increased from 0.070 to 0.077 and the generalization index from 2.21 to 2.69, suggesting more generalized feeding links. However, this was accompanied by a compressed δ¹⁵N range (11.77‰ to 10.47‰), indicating a shorter food chain, and a decline in omnivory from 65.4% to 55.2%. Isotopic data revealed greater reliance on terrestrial C3 plant-derived carbon sources. The diet of the key predator, Culter alburnus, shifted from 78.9% to 64.9%, reflecting increased use of lower-trophic-level resources. This pattern suggests that the recovery was primarily driven by enhanced primary production and terrestrial organic matter inputs, facilitated by stronger land-water coupling and Flood Pulse Concept. In conclusion, ecological recovery after a major conservation intervention such as the fishing ban is not uniform; trajectory depends on local environmental conditions such as flow velocity and floodplain connectivity. These findings underscore the critical importance of assessing functional attributes like food web structure alongside biodiversity metrics. This research provides a crucial scientific foundation for developing and implementing spatially differentiated, adaptive management in the Yangtze River Basin to improve the effectiveness of large-scale conservation efforts.