Objective To investigate the influences of Yiqi Huoxue Decotion and Bushen Shengsui Decotion on protein expressions of Jagged1、 Notch4 and Hes1 in hippocampus and frontal cortex of rats with cerebral ischemia reperfusion injury. Methods The rat model of focal cerebral ischemia/reperfusion was established by using suture method for inducing middle cerebral artery occlusion（MCAO）， the rats were randomly divided into sham group， model group， Yiqi Huoxue Decotion group（Y group） and Bushen Shengsui Decotion group（B group）. After ischemia for 2h and reperfusion， The hippocampus and frontal cortex of ischemic side were taken tissue samples in 7d and 14d. The protein expressions of Jagged1、 Notch4 and Hes1 in hippocampus and frontal cortex were detected by using Western Blot. Results The value of Jagged1、 Notch4 and Hes1 protein expressions in model group were higher than that in sham group in 7d and 14d（P<0.05）， the value of Jagged1、 Notch4 and Hes1 protein expressions in Y group and B group were lower than that in model group in 7d and 14d（P<0.05）， the value of Jagged1、 Notch4 protein expressions are significant difference between Y group and B group in 7d and 14d（P<0.05）. Conclusion Yiqi Huoxue Decotion and Bushen Shengsui Decotion can regulate the Notch signaling pathway， affect the proliferation and differentiation of endogenous neural stem cells after cerebral ischemia， make them differentiated into neurons more through reducing protein expressions of Jagged1、 Notch4 and Hes1 in hippocampus and frontal cortex.