Objective Recent studies have shown that intestinal microorganisms are associated with metabolic diseases, such as type 2 diabetes mellitus (T2DM), and the reported mechanisms are mostly based on rodent models, but rarely reported in pig models, which are closer to human biology. Methods To explore changes in composition and structure of intestinal microorganisms in a mini-pig model of T2DM, the Guangxi Bama mini-pig was provided a high-fat / high-sugar diet to induce T2DM. After successful induction of T2DM, fresh fecal samples were collected from individuals in the T2DM and control (CN group, fed a normal diet) groups, and 16S rRNA gene sequencing technology was used to analyze the composition and structure of intestinal microorganisms. Results The sequencing result showed that the diversity of intestinal microorganisms was decreased in T2DM group versus CN groups. At the phylum level, the abundance of Firmicutes and Bacteroides was significantly increased and decreased, respectively, in T2DM group compared with the CN group. At the genus level, principal coordinates analysis showed that the composition of the CN group was significantly different from that of T2DM group, and the T2DM group had a unique genus of Mitsuokella related to succinic acid production. Comparison of the two groups and linear discriminant analysis effect size analysis showed that several bacteria exhibited significant differences between the two groups, such as Oscillospira, Prevotella and Peptococcus, which were significantly enriched in the CN group, and g__Intestinibacter, which was significantly enriched in the T2DM group. There were no significant differences in metabolic pathways between the two groups. The two groups were mainly enriched in pathways assigned the biosynthesis of amino acids, carbon metabolism, amino sugar and nucleotide sugar metabolism, glycolysis and gluconeogenesis. Conclusions In this study, we found the characteristics of intestinal microorganism variation and the potential microorganisms closely associated with the occurrence of T2DM in mini-pigs. These findings provide a theoretical basis for the study of the association and related mechanisms between intestinal microorganism and T2DM .