The gut microbiota is closely related to the energy metabolism, and the disorder of its composition and metabolism can lead to insulin resistance, obesity and type 2 diabetes (T2DM) through multiple pathways. Berberine is used as an adjuvant treatment for metabolic diseases, such as obesity, T2DM, and nonalcoholic fatty liver disease, due to its effects on weight loss, hypoglycemia, lipid regulation, and other physiological parameters. Recent studies have shown that berberine can regulate the composition and metabolism of the gut microbiota, improve the gut micro-ecological environment, thereby ameliorating insulin resistance and metabolism. This review clarifies how the gut microbiota induces systemic low-grade inflammation and the development of metabolic diseases. It also explores berberine intervention in metabolic diseases, affecting the intestinal microbiota-inflammation axis, in order to find new therapeutic strategies for the treatment of such diseases and to provide important guidance for in-depth research in this field.