To investigate the effects of Huanglian Jiedu Decoction(HLJDDAF) which consists of total alkaloids, total flavonoids and total iridoids on the expression of VEGF in caudate putamen and hippocampal CA1 region of rats after middle cerebral artery occlusion and to explore the mechanism of the effects. Methods: Cerebral ischemia was induced by middle cerebral artery occlusion (MACO). The expressions of NeuN and VEGF were observed by immunofluorescence staining. Results: The expression of NeuN in distant brain regions of rats in model group were significantly reduced, and the expression of VEGF in caudate putamen and hippocampal region were reduced compared with those of the sham group（P<0.01-0.05）. Aqueous extract, total flavonoids were capable of increasing the expression of the NeuN compared with those of the model group（P<0.01-0.05）; total alkaloids, total flavonoids and total iridoids were capable of increasing the expression of the VEGF in hippocampal CA1 region compared with those of the model group（P<0.01-0.05）. Especially the total flavonoids also increased the expression of VEGF in caudate putamen（P<0.01）.Conclusion: Total flavonoids of HLJDD is inherently capable of regulating the expression of VEGF in caudate putamen and distant brain regions, and reducing hematogenously secondary damage of hippocampal CA1 region after cerebral infarction.