The present invention relates to a composition comprising metformin as an active ingredient for preventing or treating inflammatory bowel disease. The metformin compound or the metformin-etanercept (product name: Enbrel) composite according to the present invention may have excellent effects of maintaining the thickness of the small intestine and length of the large intestine normal, inhibiting or decreasing the activity of IL-17 and TNF-a, and promoting or increasing the activity of IFNr, and therefore can be effectively used as a pharmaceutical composition for preventing or treating autoimmune diseases including inflammatory bowel disease.