To observe the protective effect and mechanism of Sailuotong capsule in focal cerebral ischemia/reperfusion. The 90 min middle cerebral artery occlusion (MCAO) reperfusion model was established. The expressions of dynamin-related protein 1 ( Drp1) and optic atrophy 1 (Opa1) were tested by Western blot. The transmission electron microscope was used to observe the changes in the mitochondrial ultra-structure. The pathological morphological changes were observed through the HE staining. The immunohistochemical method was used to test Drp1 and Opa1 expressions. Sailuotong capsule (33, 16.5 mg x kg(-1), ig) can inhibit the abnormal mitochondrial fission and fusion in the cortical area on the ischemia side and the mitochondrial fission gene expression and promote the mitochondrial fusion gene Opa1 expression, so as to alleviate the energy metabolism disorder caused by ischemia/reperfusion. Sailuotong capsule can inhibit the abnormal mitochondrial dynamics in peri-ischemic regions and maintain the normal morphology of mitochondria, which may be the mechanism of Sailuotong capsule in promoting the self-recovery function in the ischemic brain region.