The differences in morphological characteristics and key genes related to flavor between wild grass carp from Jingpo Lake and commercially farmed grass carp were investigated to explore the unique aquatic germplasm resources in the Mudanjiang region. Grass carp with similar body weight were selected for morphological measurements, and their dorsal muscles were sampled for transcriptome sequencing analysis. The results showed that wild grass carp from Jingpo Lake had a more elongated body shape, a significantly lower viscerosomatic index of 7.68% (P<0.01), and a significantly higher dressed carcass ratio of 92.32% (P<0.05) than commercial grass carp. Transcriptome sequencing yielded 40.38 Gb of filtered data, revealing 1587 differentially expressed genes, including 527 upregulated and 1060 downregulated genes. These demonstrated high similarity between samples. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, 183 signaling pathways were identified. Further investigation was performed on flavor-related regulatory genes. Genes AK4 and AMPD1 played important roles in inosine monophosphate (IMP) synthesis; FASN, LPL, PLIN2, ACOX1, and FABP1a were involved in regulating intramuscular fat (IMF) accumulation; and BCAT1, BCAT2, and DDO were suggested to be key to the synthesis of flavor amino acids. In summary, wild grass carp from Jingpo Lake have a greater edible yield and less abdominal fat accumulation, attributed primarily to the expression of flavor-related genes that contribute to their unique flavor. This study provides a theoretical basis for developing and applying grass carp resources in the volcanic barrier lake system of the Mudanjiang region.