Objective To study the change principles of the oxygen free radical on the sub-cellular level in the process of ischemia-reperfusion injury. Methods The activity of superoxide dismutase(SOD) and the content of malondialdehyde(MDA) in the mitochondria and cytoplasm of rat liver with local ischemia-reperfusion were assayed. The histological changes of the liver were observed at the same time. Results The activity of SOD and the content of MDA kept rising and the histological changes of the liver cells kept aggravating in the process of ischemia-reperfusion. Conclusion The ischemia-reperfusion injury of rat liver occurred at the beginning of reperfusion and mitochondria was damaged first, however the injury action could be delayed by self defense.