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Coilia nasus is a valuable commercial migratory fish species with ecological and economic importance in China. To explore the molecular mechanisms underlying the response to food intake, the stomach transcriptomes of feeding and non‐feeding C. nasus were analysed via RNA‐seq. A total of 610,640,864 clean reads were obtained, and annotation to six databases identified 63,567 unigenes. Comparative analysis of the gene expression in feeding and non‐feeding C. nasus identified 1,968 differentially expressed genes (p <.05), including 1,180 up‐regulated and 788 down‐regulated genes. Our results showed that stomach distention activated the vagal afferent neurons, resulting in satiation. Several of the most relevant appetite genes (e.g. leptin receptor [LepR], somatostatin [SS], nucleobindin‐2 [NUCB2], 5‐hydroxytryptamine receptor [5‐HTR], growth hormone receptor [GHR]) were also involved in the regulation of food intake and led to the termination of feeding. Furthermore, significant differences were observed in the genes encoding key enzymes involved in metabolism such as the tricarboxylic acid cycle (TCA) pathways, fatty acid synthesis and glycolysis, indicating that C. nasus utilizes food for its energy and nutrient contents to support life and gonadal development. These findings provide valuable insights into the mechanisms underlying appetite and metabolic regulation in anadromous fish and create a foundation for further research on C. nasus artificial breeding and migration energetics. [ABSTRACT FROM AUTHOR]