Trachypithecus francoisi belongs to the wild animals under the first level of protection in China and is one of the most precious and rare primates in the world. Intestinal microorganisms are the most important "microbial organs" in animal body, which participate in nutrient absorption, metabolic regulation and immune function, and play a significant role in maintaining organism health and adaptive evolution. Studying the gut microbial community structure of T. francoisi in different habitats and their functions on host energy metabolism, nutritional balance and food digestion is significant for the conservation of endangered species. However, few studies have focused on the changes of intestinal microbial structure and function in different habitats, especially in captivity, resulting in unclear that due to changes in the diet of T. francoisi, and the effects. Metagenomic sequencing technology was used to compare and analyze the gut microbial community composition and function differences of wild(five individuals) and captive(four individuals) black langur monkeys in this study. The results showed that in terms of species composition, the gut core microbiota of T. francoisi was mainly Firmicutes and Bacteroidetes. The number of unique microbial communities of wild black langur monkeys was larger than that of captive group, and the species composition structure of intestinal microflora of langurs in different habitats had certain similarities and differences. The Alpha diversity index showed that there was no significant difference in gut microbial diversity and uniformity between wild and captive T. francoisi (P > 0.05). By independence test, it was found that Methanobacteriota had the most significant difference between the intestinal microbes of T. francoisi in wild environment and captive environment (P < 0.01). Functionally, most of the genes in the intestinal microbial community of T. francoisi was related to metabolism and genetic information, and there were significant differences between wild and captive T. francoisi in amino acyl TRNA biosynthesis, pyrimidine metabolism, propionic acid metabolism pathways (P < 0.05). Ruminococcus and Blautia increased the ability of T. francoisi to produce Acetyl-CoA in captivity by regulating FOX2 gene expression. This study initially revealed the effects of the wild environment and captive environment on the characteristics and functions of the gut microbial community of T. francoisi in Guizhou Province, which is helpful for scientific assessment of the physiological health status of the wild population of black langur monkeys. This study also provides theoretical basis for the gut microbiology of this rare species in the wild population protection and captive population breeding.