It is well known that a brief period of ischemia increases tolerance to a subsequent severe ischemic episode. In the present study, bilateral carotid arteries occlusion (BCAO) was applied as pre-conditioning to testify whether this kind of ischemia could preserve the function of mitochondria with the impairment induced by middle cerebral artery occlusion MCAO) in brain. The activities of respiratory enzyme complex I to IV, mitochondria swelling, membrane potential, and membrane fluidity were investigated. The results showed that the percentage of infarct area decreased greatly due to the ischemic pre-conditioning (IP) revealing the preventive effect of IP on infarct size, The activities of respiratory enzyme complex III, IV were effectively preserved (p < 0.05, p < 0.05) compared with MCAO group through ischemic preconditioning. Mitochondrial swelling and membrane fluidity were protected by IP, and also an increased trend was found in membrane potential, which indicated that the integrity of mitochondrial membrane was maintained. It suggested that the function of mitochondrial energy metabolism in brain ischemia was effectively protected by this kind of pre-conditioning.