To elucidate the trophic ecological characteristics of the fish community in the Jiangjin section of the National Nature Reserve for Rare and Endemic Fishes in the Upper Yangtze River, this study analyzed 246 individuals across 42 fish species using stable isotope analysis (SIA) of carbon (δ13C) and nitrogen (δ1?N) during the flood and dry seasons of 2024. The results revealed that: (1) At the fish community level, the δ13C values ranged from -28.76‰ to -19.05‰, showing no significant difference between the flood and dry seasons; meanwhile, the δ1?N values ranged from 3.73‰ to 13.01‰, exhibiting significant seasonal differences and reflecting clear trophic differentiation. (2) The trophic level (TL) of the fish community ranged from 1.17 to 3.82, with a mean value of 2.37 ± 0.45, illustrating multi-level trophic relationships. (3) Significant seasonal hydrological differences were observed in the community trophic structure, with overall δ1?N values and the trophic levels of major feeding guilds being significantly higher in the dry season than in the flood season(P<0.05). (4) The community trophic niche width, measured by the Standard Ellipse Area (SEAc), was significantly larger in the flood season than in the dry season, indicating seasonal hydrological differences in food resource utilization patterns. This study provides a critical perspective for understanding the food web structure, seasonal hydrological dynamics, and resource utilization strategies of the fish community in this protected area, thereby offering a scientific basis for fish biodiversity conservation and ecosystem management in the region.