Myocardial ischemia/reperfusion injury (MI/RI) is a common pathological process in ischemic heart disease and cardiac surgery. Mitochondrial injury and dysfunction are the main causes of MI/RI during ischemia/reperfusion. So far, it has found that after transplantation of intact mitochondria into the diseased tissue, the damaged mitochondria can be replaced or repaired by internalization and fusion with endogenous mitochondria, so as to enhance tissue energy metabolism, save cardiomyocytes and restore tissue function. This review introduces the isolation of exogenous mitochondria, infusion methods, and the mechanisms of mitochondrial internalization and fusion, while summarizing the latest research progress on the protection of MI/RI by mitochondrial transplantation and the effect of mitochondrial transplantation on heart transplantation. Mitochondrial transplantation provides a new therapeutic approach to protect against MI/RI.