Aim To investigate the effect of Shuxin Yimai Jian (SXYMJ) on the apoptosis and the related gene Fas antigen and Fas ligand (FasL) of vascular balloon injury in thoracic aorta in rats with stagnancy of qi and blood stasis. Methods Fifty-eight rats were randomly divided into the sham group (n=10), SXYMJ group (n=24) and the control group (n=24). The thoracic aorta endothelium was denudated in the SXYMJ and control groups. SXYMJ was given from 7 days before operation to 14 days after operation in the SXYMJ group. Fas and FasL were detected by immunohistochemistry and the apoptotic cells were stained in situ by terminal deoxynucleotidyl transferase mediated-deoxyuridine triphosphate nick end labeling. Results Apoptotic cells could be detected in the smooth muscle cell (SMC) at the 14th day after operation. The expression of Fas and FasL in the neointima was increased by SXYMJ. The apoptosis of SMC was enhanced by SXYMJ, while the neointima area was attenuated. Conclusion SXYMJ probably regulates the apoptosis of SMC through Fas system and then inhibits the neointima hyperplasia.