Objective To study the effects of ligustrazine and shear stress on the apoptosis of suspending vascular endothelial cell. Methods Rat cerebral microvascular endothelial cell (rCMEC) cultured in vitro was used. The administration of the drug incorporated with different levels of shear rate introduced by rotational cone plate shear generator. The influences of ligustrazine and shear rate on the apoptosis were determined by the immunofluorescent of Annexin V-FITC/PI with flow cytometer. Results The analysis of variance shows that ligustrazine and shear rate can affect the apoptosis rate of suspending rCMEC significantly. Ligustrazine can restrain apoptosis rate, high shear rates can raise apoptosis rate;however, there is no interaction between ligustrazine and shear rate. The t test shows that ligustrazine(31.5～126μg/ml) has no significant effect on suspending rCMEC apoptosis at zero shear rate. However, high shear rates (6000, 8000s -1 ) can induce apoptosis which can be significantly inhibited by adding ligustrazine. Conclusion The results indicate that a suitable dose of ligustrazine can distinctly restrain vascular endothelial cell apoptosis induced by high shear rates.