Acute myocardial infarction (AMI) has become the leading cause of death in cardiovascular diseases. Myocardial ischemia and reperfusion (MI/R) occurs when myocardial blood circulation is reconstructed after blood supply is limited or lack, often after myocardial infarction, and is the main cause of acute myocardial injury. According to the length of ischemia time, arrhythmia, myocardial inhibition, and myocardial infarction may occur in sequence in MI/R. Mitochondria are the key organelles involved in MI/R injury. Mitochondrial ROS eruption, Ca²⁺ imbalance, mPTP opening, mitochondrial swelling, and release of pro-apoptotic proteins all lead to mitochondrial dysfunction and myocardial function impairment. Exercise is an effective intervention to prevent myocardial ischemia-reperfusion injury, and its protective effect is closely related to the intensity of exercise, the length of exercise time, the type of exercise and the internal exercise ability. The mitochondrial mechanism of exercise protection against myocardial ischemia-reperfusion injury is determined by many factors. During reperfusion, the heart after trained is better able to maintain energy homeostasis, maintain ΔΨ_m and limit mPTP activation, maintain ATP synthesis. Activation of the sarcoK_ATP and/or mitoK_ATP channels by exercise induces cellular and/or myocardial hyperpolarization, protecting the mitochondria and myocardium during MI/R. Exercise-trained hearts can regulate calcium homeostasis during MI/R and limit mitochondrial Ca²⁺ overload. Exercise training can improve the activity of mitochondrial antioxidant enzymes to clear ROS and regulate mitochondrial Ca²⁺ concentration during MI/R. Exercise can increase the bioavailability of NO near mitochondria and indirectly achieve exercise-induced myocardial protection through protein S-nitrosylation and the eNOS-NO pathway is related to mitochondrial biogenesis after exercise training. Exercise training can also affect mitochondrial dynamics during MI/R by preventing mitochondrial division and promoting mitochondrial fusion. Exercise training can promote autophagy of damaged mitochondria and reduces apoptosis through mitochondria too, thus helping to maintain the function of mitochondrial bank. Besides these, exercise training leads to the production of motor factors (mainly from the muscles, but also from the brain, red blood cells, and other tissues) that contribute to remote regulation of the heart. This paper reviews the mitochondrial mechanism of MI/R, the protective effect of exercise on MI/R and the role of mitochondria in it, in order to provide more theoretical basis and new therapeutic targets for the diagnosis and treatment of heart disease, and provide new targets for drug research and development. In future clinical treatment, it is expected that sports pills targeted mitochondria can treat MI/R injury for bedridden people who cannot exercise or people who do not want to exercise through new technological means such as nanoparticle packaging.