The present invention relates to a composition for preventing or treating mitochondrial diseases caused by immunosuppressants, and immune diseases, containing metformin and, more specifically, to a composition for treating mitochondrial diseases caused by immunosuppressants, containing metformin; a pharmaceutical composition for preventing or treating immune diseases, containing, as active ingredients, metformin and an immunosuppressant, which is a target of rapamycin inhibitor (mTOR inhibitor); and a pharmaceutical composite formulation for preventing or treating immune diseases, containing, as ingredients, metformin and a mammalian target of rapamycin inhibitor, wherein the metformin and mammalian target of rapamycin inhibitor are administered simultaneously or separately, or administered in a predetermined sequence. The composition effectively alleviates mitochondrial dysfunction, occurring as a side effect of conventional immunosuppressants, while having a more improved immunosuppressive therapeutic effect, thereby being usable in prevention and treatment of transplant rejection, autoimmune diseases, inflammatory diseases, and the like, all of which require immunosuppression.