The upper reach of the Yangtze River is one of the regions with the richest fish biodiversity in China, and its floodplain waters, as an important part of the river ecosystem, play an important role in maintaining regional fish biodiversity. Based on the Bayesian mixture model and the SIBER method, the carbon and nitrogen stable isotope techniques were applied in the wet season (August) and the dry season (November) in 2019 to determine the seasonal variation in the consumption of food by fish in the Mituo floodplain waters and implications for food web dynamics. The results showed that in the wet season, the average value of δ¹³C of the basic carbon source was -23.02‰ (with a range from -31.01‰ to -11.2‰), and the average value of δ¹⁵N was 2.58‰ (with a range of -0.51‰-6.84‰). Moreover, the average values of δ¹³C and δ¹⁵N in the dry season were -21.93‰ and 7.22‰, respectively, and their ranges were from -26.31‰ to -15.36‰ (δ¹³C) and from 4.89‰ to 8.81‰ (δ¹⁵N). The allochthonous nutrients were identified as the main energy sources of the food web during the wet season with a trophic level length of 3.6, while the autochthonous nutrients were identified as the main contributors to energy sources in the food web during the dry season with a trophic level length of 2.6. Compared with those in dry season, fish communities in wet season had larger ecological niche space, indicating the diversification of their food sources and the utilization of different habitat types. Furthermore, the increase of basal carbon sources (CR) and habitat diversification during the wet season were found to enlarge the niche space (TA, SEAB and SEAC) for fish communities, and the niche redundancy further enhanced the ecosystem structure stability. Conversely, the decrease in the external nutrient inputs and the retreat of water level during the dry season reduced the freshwater fish diversity and niche space area. The results also showed that seasonal changes in hydrological connectivity profoundly affected the coupling pattern between consumers and food resources, biodiversity abundance, and structural stability of fish food webs, providing a useful reference for aquatic biodiversity conservation in the floodplain waters of the upper Yangtze River.