Objective To study the hypoglycemic effect of Polygonatum sibiricum polysaccharides on type 2 diabetic mice and its effects on intestinal flora and pathological structure of small intestine. Methods Fifty male mice were used, except 10 were fed normally, the others were fed with high-fat and high-sugar diet for 6 weeks, and then injected with streptozotocin intraperitoneally to make type 2 diabetes mice model. After successful modeling, they were randomly divided into model group and Polygonatum sibiricum polysaccharides (500, 250, 125 mg/kg) group and the model group mice were given normal saline. The changes of bodyweight and blood glucose of mice in each group were recorded. After 4 weeks, feces were collected and sequenced by a 16S rRNA high-throughput sequencing, and the pathological changes of small intestine were observed by HE staining. Results In diabetic mice, the weight decreased. After given Polygonatum sibiricum polysaccharides, the weight of mice increased by 14.24%,11.97% and 8.78%, and the blood glucose decreased by 26.6%, 22.3% and 13.3%, respectively after high, medium and low doses of Polygonatum sibiricum polysaccharides were administered. In addition, the pathological disorder and swelling of intestinal histopathology were improved. There were significant differences in intestinal microorganisms between the model group and the Polygonatum sibiricum polysaccharides. Verrucomicrobiae in the model group increased significantly, while the microorganism abundance of Firmicutes and Bacteroidetes in the healthy group and Polygonatum sibiricum polysaccharides group was higher. Conclusion Polygonatum sibiricum polysaccharides has a significant hypoglycemic effect on diabetic mice and a certain protective effect on their intestines, the mechanism may be achieved by increasing the richness of beneficial bacteria and improving the immune function of mice, it’s in a certain dose-effect relationship, and its immune function needs further study.