To investigate the molecule mechanism of Weinaokang in treatment of the rats with focal cerebral ischemia reperfusion by using LC-MSMS method. Methods: Global proteomics analysis had been conducted on serum samples collected from normal group, model group,and Weinaokang treatment group. After digestion, the samples were detected by applying nano Chip-ESI Ion Trap. Protein identification, pattern discrimination and relative quantitative analysis were determined using Agilent Spectral mill、scaffold 3 and SIMCA P+ software. Results: 833, 701and 798 proteins were found on healthy group, model group, and TCM treatment group respectively. Compared with healthy group, 18 changed proteins had been determined: 13 proteins up-regulated, 5 proteins down-regulated in model group, and these differential proteins had converse tendency in TCM treatment group. Current studies also aim at the major functional classification of proteins between model and health groups, as well as model and treatment groups. The biological function of these changed proteins were closely related to growth and differentiation of neurons, neuronal apoptosis, signal transduction and regulation of translation,etc. Conclusion:The molecule mechanism of Weinaokang capsule for treating focal cerebral ischemia reperfusion may be associated with different proteins, and it will provide a new idea for study of molecule mechanism of Weinaokang capsule.