As a regulatory mechanism involved in cell metabolism and organelle renewal，autophagy plays an important role in the physiological and pathological processes of the body. Mitophagy，as a type of cell target-specific autophagy，can identify and remove functionally impaired mitochondria and achieve mitochondrial quality control. Mitochondria mainly regulate autophagy through Parkin-dependent and non-Parkin-dependent pathways，thereby affecting the body’s function. Studies have shown that mitochondrial autophagy is closely related to the process of cerebral ischemia-reperfusion injury，but its role in cerebral ischemia-reperfusion injury has been controversial. This article mainly summarizes the mechanism of mitochondrial autophagy and the way in which mitochondrial autophagy participates in cerebral ischemia-reperfusion injury.