The intestinal microbiota play an important role in the life of amphibians. The composition of the intestinal microbial community may vary by developmental stage. In this study, 16S rRNA high-throughput sequencing was used to study the intestinal microbiota of Hynobius maoershanensis tadpoles and adults that exclusively inhabit the Maoer Mountain swamp at an altitude of approximately 2000 m. The results indicated that there was no significant difference in intestinal microbiota between tadpoles and adults. Nevertheless, the abundance of intestinal microbiota in adults was much higher than that in tadpoles. Specifically, at the phylum level, Bacteroidetes was more abundant in adults than in tadpoles. At the genus level, Proteobacteria, Actinobacteria, Cyanobacteria, and Planctomycetes were more abundant in tadpoles, whereas Burkholderiaceae, Caedibacter, Bacteroides, and Serratia were more abundant in adults. A functional prediction analysis revealed that there was no significant difference between tadpoles and adults; however, the function of the intestinal microbiota in H. maoershanensis includes amino acid transport and metabolism, general function prediction only, transcription, energy production and conversion, liquid transport, and metabolism. The aquatic and terrestrial living environment of tadpoles and adults may be the main reason for the difference in intestinal microbiota between tadpoles and adults. Our study provides evidence of variations in the intestinal microbiota of tadpoles and adult amphibians, highlighting the influence of historical developments on the intestinal microbiota and the need for increased understanding of the importance of physiological characteristics in shaping intestinal microbiota of amphibians, which consequently help us to understand the adaptative mechanism of amphibians from an aquatic to a terrestrial environment.