This study sought to explore the correlation between metformin and Akkermansia muciniphila (Akk), aiming to clarify the molecular mechanism of their synergistic effects. Akk standard strain JCM30893 was cultured in an optimized medium supplemented with 4 mmol/L metformin. Under this condition, we observed significant growth promotion of Akk, as evidenced by enhanced consumption of sugars and proteins and alterations in pH. Notably, metformin treatment significantly increased the production of arginine by Akk, along with an elevated production of short-chain fatty acids (butyrate, isovalerate, isobutyrate, and acetate). Untargeted metabolomics further confirmed that metformin up-regulated therapeutic metabolites, including arginine, L-carnitine, and nicotinamide, which are associated with antidiabetic, anti-inflammatory, cardiovascular protective, and anticancer properties. Additionally, metabolic pathways linked to protein digestion, nucleotide metabolism, and arginine biosynthesis were found to be enhanced in the metformin-treated group. These findings provide a molecular framework for elucidating the synergistic therapeutic effects of metformin and Akk in the treatment of diabetes and obesity, offering insights into potential combination therapies.