Abstract: To compare food-web structure and energy-flow characteristics between a spur dike area and a non-dike area in the fluctuating backwater zone of the Three Gorges Reservoir in the upper Yangtze River, field surveys were conducted in April and October 2025, combined with stable isotope analysis, the MixSIAR mixing model, and the Ecopath model. The results showed that food webs in both areas were jointly supported by grazing and detrital food chains, with primary producers and detritus representing the main energy sources. In the spur dike area, trophic levels of functional groups ranged from 1.00 to 3.29, with benthic carnivorous fish and Squaliobarbus curriculus as the main high-trophic-level groups. In the non-dike area, trophic levels ranged from 1.00 to 3.52, and additional predatory groups, including culter fish and Siniperca knerii, contributed to a relatively greater extension of the food web toward higher trophic levels. The total system transfer efficiency, as well as efficiencies based on primary producer and on detritus were 2.58%, 2.59%, and 2.57% in the spur dike area, respectively, which were lower than the corresponding values in the non-dike area (3.50%, 3.50%, and 3.49%). Total system throughput, connectance index (CI), Finn’s cycling index (FCI), and Finn’s mean path length (FML) were all higher in the non-dike area, whereas ascendency (A) was slightly higher in the spur dike area, suggesting that energy flow in the spur dike area was more concentrated along a limited number of major pathways. Mixed trophic impact and keystone analyses indicated that high-trophic-level regulation in the spur dike area was mainly associated with benthic carnivorous fish and S. curriculus, whereas that in the non-dike area involved benthic carnivorous fish, S. knerii, and culter fish. The Pedigree indices of the Ecopath models for the spur dike and non-dike areas were 0.517 and 0.514, respectively. Sensitivity and Monte Carlo analyses suggested that the relative differences in FCI and CI between the two areas were comparatively stable, whereas differences in the system omnivory index (SOI) and A were limited. Overall, at the present survey scale, the spur dike area was characterized by more concentrated basal-resource pathways and high-trophic-level regulation, while the non-dike area exhibited greater energy-flow magnitude, stronger trophic connectivity and a higher capacity for energy transfer to higher trophic levels. These findings provide a case-study reference for food-web analysis and ecological-effect assessment of spur dike waters in the upper Yangtze River.