Objective To investigate dynamic changes of complement (C1q and C3d) expression during cerebral ischemia-reperfusion injury and its correlation with brain injury , and to discuss its possible mechanisms. Methods The middle cerebral artery occlusion (MACO) model was induced through filament method. Immunohistochemical method was used to detect complement (C1q and C3d)expression. The dynamic changes of neurological deficit scores and brain water content was recorded. Results The complement (C1q and C3d) expression increased gradually after local cerebral ischemia-reperfusion injury, peaked at 24h after ischemia-reperfusion ,and returned to normal at 120h after reperfusion. Brain water content was highest at 24 to 72 h after reperfusion. The time point of the most severest neurological deficit was at 24 h after reperfusion. The complement (C1q and C3d)expression was positively correlated with brain edema and neurological deficit. Conclusions The activation of complement may participate in the course of the injury after ischemia-reperfusion, so inhibition of complement is likely to be the target of treatment.