Abstract: We aimed to investigate the effects of differential proteomics of hippocampal mitochondria in different hypothermic circulation arrest,and to discuss the protection to brain with deep hypothermic circulation arrest.The cardiopulmonary bypass model was established by puncture through jugular vein and caudal artery with 16G canal and 22G detained needle respectively.Then we extracted the hippocampus in every groups after finishing circulation arrest 10 minutes at normal brain temperature（35.537.5 ℃,NTCA）group and deep hypothermic brain temperature（27 ℃,DHCA）except the normal contract group(sham group,35.537.5 ℃,NC).The hippocampal mitochondria was separated and observed by electron microscope,the results showed that the purity and integrity of mitochondria were high and the sample was suited to next experiments.The preliminary experiment of SDS-PAGE showed that the sample was qualified to analysis of isobaric tags for relative and absolute quantification(i-TRAQ) and liquid chromatography-mass spectrometry (LC-MS/MS).We screened 7 differential protein (the changes of expression dose 1.5 or 0.67；p0.05),and then made the further study about one of the differential protein-cytochrome C oxidase.The semi-quantitative study by Western-blot to the sample of hippocampus slice showed no changes in dose totally（p0.05）among 3 groups,at the same time the qualitation study revealed different translocation of COX protein from mitochondria to cytoplasm between NTCA group and DHCA group.So we concluded that DHCA could mitigate hypoxic-ischemic brain damage was relevant with the release of cytochrome C oxidase in hippocampal mitochondria from mitochondria to cytoplasm in acute stage.