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Gut microbes are closely related to physical health. The intestinal microbial population in fish is a complicated ecological environment that plays an important role in the digestion and absorption of nutrients and fish health. As a unique species in Tibet, Schizothorax o'connori has a protective value for the ecological balance of plateau rivers. However, with the reproduction of invasive fish species, the population of S. o'connori has declined significantly. Therefore, we used 16S ribosomal DNA (rDNA) sequencing techniques to analyze the composition and diversity of intestinal microbiota in S. o'connori at different growth stages, which can contribute to sustainable reproduction and survival of S. o'connori. The results showed that the diversity of intestinal microflora increased with the growth of S. o'connori. A total of 24 phyla, including the four predominant phyla Proteobacteria, Verrucomicrobia, Firmicutes, and Bacteroidetes, were detected, and 292 genera, including the three predominant genera Pseudomonas, Moraxellaceae, and Geobacillus, were identified. These results confirm that the ability to decompose fibers and utilize carbohydrates in feeds was enhanced. Intestinal health and immunization status were improved with the growth of S. o'connori. Different growth stages significantly affected the microbial community structure of the intestinal tract of S. o'connori. [ABSTRACT FROM AUTHOR]