Tree shrew is a new type of experimental animal model with broad application potential. However, the current distribution of intestinal bacteria and pathogens in the wild Tupaia belangeri yaoshanensis (T.b. yaoshanensis) in Guangxi are still unclear. Therefore, we performed for the first time the isolation and identification of the bacteria cultured in the subspecies of the wild T.b. yaoshanensis in Guangxi. Thirty-five strains of bacteria were isolated from 19 T. b. yaoshanensis subspecies and identified by 16S rRNA sequence analysis. There are 20 species of bacteria in 13 genera and 7 families, and the main flora in the intestinal tract of the wild T. b. yaoshanensis in Guangxi include Escherichia coli, Citrobacter freundii, and Proteus mirabilis. Moreover, to study the drug susceptibility of intestinal bacteria isolated from the feces of T.b. yaoshanensis collected from Dayaoshan in Guangxi, a drug sensitivity test was conducted using some of the isolated intestinal bacteria. The intestinal bacteria of T.b. yaoshanensis were sensitive to ceftazidime, gentamicin, and levofloxacin, and resistant to cefazolin and sulfamethoxazole. This is the first to grasp the diversity and potential pathogenicity of the fecal flora of the wild T. b. yaoshanensis in Guangxi. These result provide the scientific basis for the isolation and quarantine of T.b. yaoshanensis, laboratory feeding, and the prevention and treatment of common digestive tract diseases.