Abstract: To explore the protective effect of benzoylpaeoniflorin (BP), an active component of Paeonia lactiflora, on cerebral ischemic reperfusion injury (CIRI) in rats and its molecular mechanism, middle cerebral artery occlusion and reperfusion (MCAO/R) model was established, and oxygen-glucose deprivation/recovery (OGD/R) model was established by using rat adrenal pheochromocytoma nerve cells (PC12) to carry out experimental research. The results show that BP can significantly improve the neuronal apoptosis induced by CIRI, reduce the area of cerebral infarction, the neuronal damage in hippocampus, the loss of Nissl bodies and the mitochondrial damage. Western blot results showed that BP could significantly down-regulate the expression of pro-apoptosis proteins (Caspase3, Bax) and up-regulate the expression of anti-apoptosis protein (Bcl-2). qRT-PCR showed that BP down-regulated the gene expression levels of pro-inflammatory factors (TNF-α, IL-1β, IL-6) and pro-apoptosis proteins (Caspase3, Bax), and up-regulated the expression level of anti-apoptosis protein (Bcl-2). Transcriptome analysis showed that the differential genes regulated by BP were mainly concentrated in TNF signaling pathway, rheumatoid arthritis, IL-17 signaling pathway and so on. To sum up, BP can reduce inflammatory reaction and oxidative stress, inhibit neuronal apoptosis, and alleviate the nerve injury of CIRI in rats, which provides experimental basis for the clinical application of BP in the treatment of ischemic stroke. All experimental procedures were approved by the Experimental Animal Ethics Committee of Zhejiang Chinese Medical University (approval number: 20241209-15).