Coilia nasus is an important economic species in the Yangtze River. It is mainly distributed in the East China Sea, the Yellow Sea, the Yangtze River, the Qiantang River, and other river basins in China. However, with economic growth, pollution and overfishing in the Yangtze River have been increasing, resulting in serious damage to C. nasus spawning grounds and a gradual decline in resources. In recent years, with the steady implementation of the ten-year ban on fishing in the Yangtze River, the C. nasus populations and those of its prey organisms have increased and were restored, and the feeding of C. nasus may have changed to some extent. To explore the trophic structure characteristics of C. nasus in the Yangtze River Estuary, 247 samples were collected by bottom trawling in summer (August) and autumn (November) of 2023, and the trophic level and niche were analyzed using stable carbon and nitrogen isotopes. The results showed that the δ¹⁵N values of C. nasus in the Yangtze River Estuary ranged from 11.70‰ to 16.39‰, with a maximum difference of 4.69‰ and an average value of (13.80±1.14)‰, which was significantly positively correlated with body length. The δ¹³C value ranged from −33.24‰ to −21.15‰, the maximum difference was 12.09‰, and the average value was (−26.35±2.60)‰, which was significantly negatively correlated with body length. According to the δ¹⁵N value, the average trophic level of C. nasus was 3.23±0.33, which was significantly positively correlated with body length. The trophic niches of C. nasus in summer and autumn were similar, and the total niche space (TA) and core niche (SEAc) overlapped. The niche breadth of C. nasus in autumn was larger than that in summer. Stable isotope analysis suggested that the feeding habits of C. nasus change during growth. With increasing body length, C. nasus tend to feed on increasingly higher trophic levels of food organisms. The results provide a basis for elucidating the feeding characteristics of C. nasus in the Yangtze River Estuary and also constitute a reference for protecting C. nasus populations and analyzing the food web energy flow in the Yangtze River Estuary.