Ershi-wei Chenxiang pills (ECP) or Aga Nixiu wan (ཨ་གར་ཉི་ཤུ།), composed of 20 Tibetan medicines, has the effect of promoting blood circulation to remove blood stasis. As a common and frequent prescription used by traditional Tibetan medicine in clinical treatment of Longzhibu disease (cerebral ischemia sequelae), it has a significant effect. However, its anti-cerebral ischemia mechanism is still unclear. The chemical components of ECP were determined by high-performance liquid chromatography and gas chromatography-mass spectrometry. SD rats were randomly divided into Sham, MCAO, Nim (20.00mg/kg), and ECP (1.33 and 2.00g/kg) groups, with 13 animals in each group. After 14 days of oral administration, we established a model of cerebral ischemia reperfusion injury by blocking the middle cerebral artery of rats. After 24h of reperfusion injury, we evaluated the protective effect of ECP on ischemic brain by neural function score, TTC, H&E and Nissl staining. TUNEL fluorescence, western blot and immunohistochemistry were used to detect the phenomenon of apoptosis and the expression of apoptosis-related proteins Bax, Bcl-2, Cyto-c and activated Caspase-3. Furthermore, western blot, qRT-PCR and immunohistochemistry were employed to detect CaMKⅡ, ATF4 and c-Jun gene and protein expression. ECP contains agarotetrol, eugenol, oleanolic acid, ursolic acid, dehydrodiisoeugenol, hydroxysafflor yellow A, kaempferide, gallic acid, alantolactone, isoalantolactone, costunolide, dehydrocostus lactone, brucine, strychnine, echinacoside, bilirubin and cholic acid. Compared with MCAO group, ECP can significantly ameliorate the neurological deficit of cerebral ischemia in rats and reduce the volume of cerebral infarction. Pathological and Nissl staining results showed that ECP sharply inhibited the inflammatory infiltration injury of neurons and increased the activity of neurons in comparation with the MCAO group. TUNEL fluorescence apoptosis results confirmed that ECP obviously inhibited the apoptosis of neurons. Meanwhile, the results of immunohistochemistry and western blot demonstrated that EPC can dramatically inhibit the expression of pro-apoptotic proteins Bax, Cyto-c and activated Caspase-3, while increase the level of anti-apoptotic protein Bcl-2. In addition, compared with MCAO group, CaMK Ⅱ gene and protein expression were improved significantly by ECP administration. while, the expression of ATF4 and c-Jun genes and proteins were decreased. In conclusion, this study preliminarily demonstrated that the protective effect of ECP on ischemic brain is related to the improvement of neurological deficit, reducing the size of cerebral infarction, improving the activity of neurons, inhibiting the mitochondrial apoptosis pathway by regulating the protein expression of CaMKⅡ, ATF4 and c-Jun. However, further in vivo and in vitro investigations are still needed to clarify the underlying mechanism of ECP in treating cerebral ischemia sequelae.