Abstract: Triplophysa rosa is a typical cave-dwelling fish distributed at Wulong County, Chongqing, China. It has degenerated eyes, albino skin, and highly developed sense organs, but its gut microbial function adapted to cave remains to be settled. The aims of this study were to analyze the structure and diversity of intestinal microorganisms in T. rosa and to explore the function of intestinal microorganisms. We extracted total intestinal DNA of 5 T. rosa, and then sequenced the V3—V4 region of 16S rRNA using Illumina Miseq sequencing technology. The number of operational taxonomic units (OTUs) of intestinal microorganisms was counted to analyze species composition, abundance, and Alpha diversity. The function of intestinal microorganisms was predicted by PICRUSt. A total of 451 OTUs of the high-quality sequences were obtained, belonging to 19 phyla, 31 classes, 87 orders, 146 families, 253 genera, and 320 species. At the phylum level, Proteobacteria, Actinobacteria, and Bacteroidetes were the dominant microorganisms. At the genus level, Aeromonas, Edwardsiella, Plesiomonas, and Shewanella were the main microorganisms. Functional prediction showed that most of the genes encoded by intestinal microorganisms are related to metabolism with the highest relationship with “amino acid transport and metabolism” and “carbohydrate transport and metabolism”. The composition of the microorganisms in the intestinal tract of T. rosa is complex, and functional analysis is helpful to understand the influence of intestinal microorganisms on its feeding, providing a theoretical basis for further study on fish diet.