Objective To investigate the effects of beinaglutide combined with Bifidobacterium quadruple viable tablets in the treatment of obese patients with type 2 diabetes mellitus (T2DM) and its impacts on metabolism and intestinal flora balance. Methods A total of 77 obese patients with T2DM were selected as research subjects and were divided into a single group (n=38) or a combined group (n=39) by the random number table method. Based on conventional treatments such as diet control, reasonable exercise, lipid reduction, and glucose control, the single group was treated with Bifidobacterium quadruple viable tablets, the combined group was treated with beinaglutide and Bifidobacterium quadruple viable tablets, and both groups were treated continuously for 8 weeks. The clinical efficacy, metabolic indexes, inflammatory factor levels, oxidative stress indicators, changes in intestinal flora, and occurrence of adverse reactions were compared between the two groups. Results After 8 weeks of treatment, the total effective rate in the combined group was higher than that in the single group (P<0.05); the combined group had lower levels of fasting blood glucose, total cholesterol, triacylglycerol, low-density lipoprotein cholesterol, C-reactive protein, endothelin-1, interleukin-6, and F2-isoprostanes, as well as smaller numbers of Bacteroides, Enterobacter, and Enterococcus in feces, than the single group, and had higher levels of high-density lipoprotein cholesterol, glutathione peroxidase, and superoxide dismutase, as well as larger numbers of Bifidobacterium and Lactobacillus in feces, than the single group (all P<0.05). There was no statistically significant difference in the incidence of adverse reactions during the treatment between the combined group and the single group (P>0.05). Conclusion Beinaglutide combined with Bifidobacterium quadruple viable tablets can improve the clinical efficacy and the metabolism of glucose and lipids, reduce the levels of inflammatory factors, relieve the oxidative stress response of the body, and regulate the intestinal flora, with a high safety in the treatment of obese T2DM.