Burdock has previously been reported to have anti-diabetic effect. Gut microbiota is an important indicator of diabetes. This study investigated the effect of burdock root powder on the diversity and composition of gut microbiota in hyperglycemic rats. Moreover, the nutritional content, biological activities and beneficial metabolites production of burdock powder during in vitro digestion are determined to supplement its anti-diabetic effect. Our results showed that burdock powder improved intestinal flora diversity in diabetic rats significantly (p < 0.05). Abundance of Lactobacillales, Firmicutes, Peptostreptococcales-Tissierellales, Peptostreptococcaceae, Enterococcaceae and Romboutsia was increased. The abundance of Erysipelotrichales and Turicibacter decreased. Inhibitory activities of α-glucosidase and α-amylase of burdock reached the highest at intestinal and gastric digestion stages (p < 0.05), respectively. Burdock can regulate the intestinal flora of hyperglycemic rats, prompting the production of acetic acid and butyric acid in their feces.