Abstract: In order to better manage the breeding of Thamnaconus septentrionalis, the structure differences of muscle quality and gut microbial flora between wild and cultured Thamnaconus septentrionalis were compared. The results showed that the holding water, holding fresh, rot resistance ability of the wild between wild and cultured Thamnaconus septentrionalis was better than that of breeding Thamnaconus septentrionalis, the difference in amino acid composition and content was not significant for both Thamnaconus septentrionalis, while the content of polyunsaturated fatty acids of wild Thamnaconus septentrionalis was significantly higher than breeding fish（P＜0.05）. The dominant intestinal bacterial phylum in Thamnaconus septentrionalis was Proteobacteria, Firmicutes, Actinobacteriota, and Bacteroidota,and Ascomycota was the predominant fungal phylum. Eubacterium, Norank-f-Mycoplasmataceae, Lactobacillus and Brevundimionas were the dominant intestinal bacterial genus, and Saccharomyces was the dominant fungal genus. The structure and relative of intestinal flora in the breeding environment changed significantly compared with those in the wild environment. At phylum level, the relative abundance of Bacteroidetes and Fusobacteria in cultured Thamnaconus septentrionalis was significantly lower than in wild ones, while the relative abundance of Fungal Basidiomycota and Chytridiomycota was higher than that in wild ones. At genus level, the relative abundance of Flavobacterium and Acinetobacter in the cultured Thamnaconus septentrionalis was higher than that in the wild Thamnaconus septentrionalis, Rhizopus was significantly higher than the wild, while the relative abundance of Mycoplasmataceae was significantly lower than wild Thamnaconus septentrionalis,and Saccharomyces and Aspergilus were lower than the wild. Compared with cultured Thamnaconus septentrionalis, the muscles of wild Thamnaconus septentrionalis are more juicy, tender, and have higher levels of essential amino acids and fatty acids. The breeding environment causes changes in the gut microbiota of Thamnaconus septentrionalis at both phylum level and phylum level. This result can provide basic data and reference for the subsequent research and breeding management of gut microbiota in Thamnaconus septentrionalis.