This study aims to clarify the disruption of gut barrier and dysbiosis of the microbiota in an experimental macaque model with 6-year diabetes mellitus (DM), and provide evidence for the application of therapeutic strategies targeting the human microbiota in the future. A single intravenous injection of high-dose streptozotocin was used to induce the type 1 diabetes (T1D) macaque model. Hematoxylin-Eosin (HE) and Periodic Acid Schiff (PAS) staining were conducted to observe colon morphological changes. The composition of gut microbiota was detected using 16S rRNA gene sequencing, and bioinformatics analysis was adopted to predict alterations in the microbial phenotype and function. Obvious intestinal inflammation and decreased goblet cells were observed in T1D macaques. 16S rRNA gene sequencing suggested a significantly different β diversity of the microbiota in the T1D group, where expanded Proteobacteria (dominantly Escherichia-Shigella) and Actinomycetota (formerly known as Actinobacteria) replaced the dominance of Bacillota (formerly known as Firmicutes) and Bacteroidota (formerly known as Bacteroidetes), indicating an imbalance in the microbial composition. Archaea was identified as a biomarker between groups. Moreover, with the reduction of beneficial bacteria (Lactobacillaceae) and the increase of pro-inflammatory bacteria and opportunistic pathogens (Enterobacteriaceae), the phenotypes of the microbiota were reversed, resulting in abnormal up- (e.g., carbohydrate and amino acid metabolism) or down-regulation (e.g., protein digestion and absorption) of multiple metabolic pathways. There were intestinal structural disorders and gut microbiota dysbiosis in T1D macaques, indicating that strategies targeting gut microbiota may be effective to treat metabolic diseases like DM.