Diseases related to cerebral ischemia are main causes of mortality and morbidity in China. Most of them are mainly caused by hypertension associated thrombosis and thrombus embolism. The principle of cerebral ischemia treatment is to promptly restore blood perfusion of the ischemic area. But in some cases, the restoration of blood flow after ischemia can not restore tissue functions, instead tissue damage and dysfunction are more serious, namely ischemia-reperfusion (I/R) injury. So to better understand the mechanism of promoting or preventing neuron death during ischemia-reperfusion injury is critical. The article mainly reports new studies on autophagy about its regulation and roles in cerebral I/R injury.