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Aim of the study: To evaluate the effects of Tong-Qiao-Huo-Xue Decoction (TQHXD) on the Blood-Brain Barrier (BBB) permeability and the constituents in the cerebrospinal fluid on the rats with cerebral ischemia injury.Materials and Methods: Cerebral ischemia rats were induced by middle cerebral artery occlusion (MCAO).Adult male Sprague-Dawley (SD) rats were randomly divided into seven groups: sham-group; model group; Nimodipine (NMP)-treated group; Nao Mai Tai (NMT)-treated group and TQHXD-treated group (3, 6 and 12g/kg body weight); The neurological function of rats was estimated by neurological defect scoring after the 1 day,7 days and 15 days after administration.Histological structure of the brain in rats were observed by hematoxylin and eosin (H&E) staining.Ultramicrostructural features of hippocampus neurons and the opening of tight junction (TJ) of BBB in rats were observed by Transmission Electron Microscope (TEM).Western blot was performed to detect the expression of ZO-1, Occludin, claudin-5, AQP-4 and MMP-9 in BBB after cerebral ischemia injury.Component analysis experiments: Adult male SD rats were randomly divided into four groups: Distilled water was administered intragastrically sham-operated rats (A); Distilled water was administered intragastrically model rats (B);TQHXD was administered intragatrically sham-operated rats (C); TQHXD was administered intragestrically model rats (D).G-C and HPLC was developed for determination of three compounds, namely, Muscone, Ligustilide and Hydroxysafflor yellow A, in rats Cerebrospinal fluid (CSF) after oral administration of TQHXD.Finally,biological samples in each group were compared with each botanical, resulting we cleared the three compounds come from which herb.Results: TQHXD significantly reduced the neurological defect scores.Histological examination indicated that dense neuropil and largely surviving neurons were seen in TQHXD-treated rats.Transmission electron microscope observation revealed that TQHXD could significantly inhibit the damage of hippocampal neurons and reduce the opening of TJ.The decreased protein expression levels of claudin-5, occludin, ZO-1 and the increased protein expression levels of AQP-4 and MMP-9 in cerebral ischemia tissue were significantly prevented by treatment of TQHXD.Analysis of experimental results showed that Muscone, Ligustilide and Hydroxysafflor yellow A could penetrate the Blood-brain barrier into the CSE while the content of the normal groups was higher than the model groups.Conclusion: These results demonstrated that TQHXD may act as a potential neuroprotective agent against BBB damage for cerebral ischemia through the protection of hippocampus neurons, the reduction the opening of TJ and decrease the permeability of BBB by up-regulating ZO-1, Occludin, Claudin-5 expressions, down-regulating AQP-4 and MMP-9 expressions.Beside, Muscone, Ligustilide and Hydroxysafflor yellow A might be the therapeutic material basis of TQHXD.