Abstract: As a unique carnivorous groundfish in the middle and upper reaches of the Yellow River basin, Silurus lanzhouensis has a delicious meat quality, a large market demand and a promising breeding prospect. Because of its characteristics of feeding on live bait such as small fish and shrimps in natural waters, it is difficult to transform the breeding domestication, and the survival rate of fry breeding is low, which becomes an important bottleneck limiting the sustainable development of the S. lanzhouensis breeding industry. This study was conducted to predict the composition, abundance, diversity and function of the intestinal flora in different environments by high-throughput sequencing of the bacterial 16S rDNA V3—V4 region of the S. lanzhouensis population in different habitats. The results showed that the main phyla of the intestinal tract in S. lanzhouensis were Proteobacteria, Fusobacteria, Firmicutes, Bacteroidetes and Actinobacteria, and the main genera were Cetobacterium, Plesiomonas, Aeromonas, Methylobacterium, Escherichia-Shigella, Acinetobacter and Shewanella. Among them, Fusobacteria and Proteobacteria accounted for more than 60% of the four groups of species and were the core phyla; the core genera were Cetobacterium and Plesiomonas. The results of gut flora α and β diversity analysis showed that the richness and evenness of the gut flora were CT>DK>WX>TL; the diversity of gut flora species was different between the two groups of culture type; the diversity of gut flora was higher in S. lanzhouensis at 26.5℃ than that at 20℃; the diversity of gut flora was lower in S. lanzhouensis in single species net tank culture than that in other culture modes. Further analysis of the composition and abundance of the intestinal flora of S. lanzhouensis showed that the relative abundance of Bacteroidetes in the CT group was significantly different from the TL group (P≤0.01) and the WX group (P≤0.05), while the relative abundance of Actinobacteria in the cultured CT group was significantly higher than that in the wild-type groups (P≤0.05), and the abundance of Methylobacterium was significantly higher than that in the WX and TL groups (P≤0.05). Further analysis in combination with environmental factors indicated that temperature, pH and ammonia concentration may be important factors influencing the composition and abundance of the intestinal flora in S. lanzhouensis. The predicted intestinal flora function indicated that different environments would affect the metabolic capacity of the intestinal flora of S. lanzhouensis. Among them, the DK group was a separate branch and its gut flora had higher abundance of lipid metabolism and carbohydrate metabolism pathways, which may be related to the higher F/B ratio of wild-type S. lanzhouensis gut flora to help the host to digest food more efficiently for more energy in the wild environment. In summary, different growth environments have significant effects on the composition, abundance, and predicted flora function of the S. lanzhouensis gut flora, which can help to promote sustainable S. lanzhouensis farming by changing external conditions and thus effectively controlling the S. lanzhouensis gut flora.