ETHNOPHARMACOLOGICAL RELEVANCE: Tongmai granules (TMG) is composed of Salvia miltiorrhiza Bge., Radix puerariae Lobata., and Ligusticum chuanxiong hort. TMG is mainly used for ischemic cardiovascular, cerebrovascular diseases, atherosclerosis, coronary heart disease, cerebral infarction and cerebral ischemia. TMG is a kind of traditional compound granule, which has a protective effect on brain injury. However, the potential protective mechanism of the TMG has not been elucidated. AIM OF THE STUDY: TMG has a good effect on brain injury, but its brain protective mechanism is still unclear. The purpose of this study was to confirm the neuroprotective mechanism of TMG, reveal its target genes and identify the active components of TMG. MATERIALS AND METHODS: High-performance liquid chromatography (HPLC) was used to identify the fingerprint of TMG. UPLC-Q-TOF-MSE was used to analyze the base peak intensity (BPI) chromatograms of TMG. TMG was pre-administered for one week, brain injury and edema were induced by injection of glutamate (Glu) into the lateral ventricles of rats. HE staining was used to investigate the pathological damage caused by Glu in the hippocampus of rats, and the RNA-seq was used to analyze the changes of different genes before and after TMG treatment. Finally, changes of related proteins were analyzed by qRT-PCR, Western blot, and other molecular biological methods. Dosage of TMG were set to 0.6 g/kg, 1.2 g/kg and 2.4 g/kg. RESULTS: We found that TMG contained many active components, including salvianolic acid, puerarin, ferulic acid, etc. TMG could improve cerebral edema and brain injury induced by Glu. After TMG treatment, differential gene analysis showed that differential genes were significantly enriched in toll-like receptor signaling pathway. qRT-PCR validation results were consistent with RNA-Seq analysis results. Combined with Western blot analysis, we found that TMG ultimately regulated the expression of inflammatory cytokines by affecting the TLR4/MyD88/AP-1 pathway. CONCLUSIONS: In this study, we combined TMG with RNA-seq analysis to demonstrate that TMG may play a neuroprotective role by regulating Toll-like receptor signaling pathway and down-regulating the expression of inflammatory cytokine. TMG may become a kind of traditional Chinese medicine with neuroprotective potential.