The mechanism of myocardial ischemia-reperfusion injury (MIRI) has not been fully elucidated nowadays, and the measures which are taken based on the existing mechanism have not achieved ideal myocardial protection effects. Therefore, it is crucial to further deepen its mechanism research and find new therapeutic targets. Mitochondrial dysfunction is closely related to myocardial energy metabolism disorder, myocardial cell necrosis and apoptosis, and it plays a key regulatory role in the occurrence and development of MIRI. This review has mainly elaborated the relationship between MIRI and mitochondrial kinetics, autologous mitochondria transplantation, cardiolipin, mitochondrial permeability transition pore and mitochondrial adenosine triphosphate (ATP)-sensitive potassium channel, thereby providing new directions and ideas to develop remedy for MIRI in the future.