Myocardial ischemia reperfusion injury is a pathophysiological process that causes damage to myocardial structure and dysfunction, and further development leads to multi-organ dysfunction of cascade. Mitochondria is an organelle that is complex in structure and responsive to external environment, and its steady state depends on the relative stability of normal form, function and quantity. Mitochondrial quality and metabolic abnormalities are closely related to the occurrence of cardiovascular diseases, especially myocardial ischemia reperfusion injury. MicroRNAs are the regulatory factors that have important role in myocardial mitochondrial protection during ischemia reperfusion injury in recent years. In this paper, the regulation mechanism of mitochondrial morphology, function, mitochondrial autophagy and mitochondrial DNA by microRNAs were reviewed. It provides a theoretical basis for the follow-up study of microRNA in ischemia reperfusion myocardial mitochondrial injury.