Guanxinning, a modern Chinese medicine preparation composed of Salviae Miltiorrhizae Radix et Rhizoma and Chuanxiong Rhizoma, has the activities of activating blood circulation, resolving blood stasis, dredging vessels, and nourishing the heart. Clinical studies have demonstrated that Guanxinning has therapeutic effect on ischemic stroke, while the specific mechanism remains to be clarified. In this study, the potential mechanism of Guanxinning against cerebral ischemia-reperfusion injury in mice was explored and then verified in vitro. The mouse model of cerebral ischemia-reperfusion injury was established with middle cerebral artery embolization(MCAO) method. The pharmacological effects of Guanxinning on the model mice were investigated based on neurological function score, cerebral infarction area, pathological morphology, neuron injury, and apoptosis. The results showed that Guanxinning lowered neurological functional score, reduced cerebral infarction area, and ameliorated the histopathological morphology, neuronal damage, and apoptosis in the model mice. RNA samples were extracted from brain tissues and subjected to RNA sequencing(RNA-seq). The differentially expressed genes(DEGs) were screened with the thresholds of ■. GO function enrichment analysis and KEGG pathway enrichment analysis were performed for the 297 common DEGs, which indicated that Guanxinning may regulate the inflammatory response, oxidative stress response, energy metabolism, and apoptosis to treat cerebral ischemia-reperfusion injury in mice. Guanxinning exerted protective effect through inhibiting inflammation and reducing oxidative stress in hypoxia/reoxygenation injured SH-SY5 Y cells. Furthermore, Western blot indicated that Guanxinning down-regulated the protein levels of p-NF-κB p65 and p-p38 MAPK and up-regulated those of PPARγ and PGC-1α. The findings suggested that Guanxinning may inhibit inflammation and reduce oxidative stress by suppressing TNF signaling pathway and activating PPAR signaling pathway, thereby exerting the therapeutic effect on cerebral ischemia-reperfusion injury in mice. This study preliminarily reveals the mechanism of Guanxinning against cerebral ischemia-reperfusion injury and provides a basis for clinical application of Guanxinning.