Abstract: In order to investigate the digestive system characteristics of subadults of Brachymystax tsinlingensis (Li, 1966) in different populations, and to provide a reference for its large-scale artificial breeding, resource conservation and utilization, we analyzed the characteristics of intestinal tissue, digestive enzymes, antioxidant enzymes and diversity of intestinal microbiota of the second filial generation of artificially bred B. tsinlingensis (Bt), body length (15.40±0.82) cm, body mass (51.50±11.90) g and the wild population in natural habitats (WBt), body length (18.17±2.57) cm, body mass (85.68±34.85) g by histological method and 16S rRNA high-throughput sequencing techniques. The results show that the intestinal tissues of Bt and WBt had the same structure, and both had intestinal glandular tissues. The thickness of the muscularis propria of WBt was significantly higher than that of Bt (p<0.05). There was no significant difference in the activity of intestinal digestive enzymes (p>0.05), and the activity of intestinal superoxide dismutase was significantly higher in Bt than in WBt (p<0.05). The dominant phyla of the intestinal flora of Bt and WBt were similar, and both of them were dominated by the phyla of Ascomycetes and Thick-walled phyla. However, the dominant genera of the bacteria differed greatly, and the dominant genera of the bacteria in Bt were the genera of aeromonas, Clostridium narrowly_18 (Clostridium_sensu_stricto_18) and Novosphingobium, while the dominant genera in WBt were Yersinia and ZOR0006. BugBase phenotypic predictions showed higher abundance of Gram-negative bacteria, aerobes, mobile elements, potential pathogens and parthenogenetic anaerobes in Bt, but the opposite for Gram-positive and anaerobes. The study show that the intestinal development, digestive and absorptive capacity, resistance to oxidative stress, and microbial diversity of the wild population of B. tsinlingensis were higher than those of the second filial generation, but the intestinal flora-induced of the second generation was less pathogenic.