The objective of the study was to explore the mechanisms by which Tongmaiyizhi capsule stabilises vulnerable atherosclerotic plaques within innominate artery of apoE-knockout mice. Our research detected the effects of Tongmaiyizhi capsule on the expression of matrix metalloproteinases (MMPs) and the constituents in vulnerable atherosclerotic plaques. 24 8-week-old apoE-knockout mice were randomly divided into two groups: capsule group and control group. They were all fed western feedstuffs for 32 weeks, and meanwhile Tongmaiyizhi capsule (720 mg/kg/d) and physiological saline were administrated respectively to the mice in these groups, after which the innominate artery was removed from the mice to be observed in regard to the morphological changes of atherosclerotic plaques with immune histochemistry, The Movat pentachrome and Sirius red staining, while thoracic aorta was removed to be stained by Oil red O for plaque count, and abdominal aorta to be analysed for the expression of MMP-2,9 and galecin-3/MAC-2. By comparison with control group, the capsule decreased atheroma by significantly reducing the expression of MMP-2,9 and increasing the collagen content in plaques. The results show that Tongmaiyizhi capsule has the ability to decrease the expression of MMP-2,9 and to inhibit atheroma so it can stabilise vulnerable atherosclerotic plaque.