Stroke is an acute cerebrovascular disease caused by the sudden rupture of cerebral blood vessels or vascular obstruction from brain tissue damage or dysfunction, thereby preventing blood flow into the brain. Cerebral ischemia-reperfusion injury (CI/RI), a common syndrome of ischemic stroke, is a complex pathological process whose physiological mechanism is still unclear. Qishiwei Zhenzhu pills (QSW), a famous Tibetan medicine preparation, has the effect of tranquilizing by heavy settling, dredging channels and activating collaterals, harmonizing Qi and blood, restoring consciousness, and inducing resuscitation. Here, we investigated the protective effect of QSW on CI/RI in rats and its potential mechanism. First, the volatile and liposoluble components in QSW were determined using gas chromatography-mass spectrometry (GC-MS). After 24 h of CI/RI, the neuroprotective effect was determined by evaluating the neurological function, cerebral infarction, histopathology, and blood-brain barrier (BBB) function. Immunofluorescence, real-time quantitative PCR (RT-qPCR), and western blot (WB) were used to detect the expression of matrix metalloproteinase 9 (MMP-9), claudin-5, and occludin. Finally, GC-MS metabonomics was used to identify different metabolites and analyze metabolic pathways. The results showed that 88 volatile components and 63 liposoluble components were detected in QSW. Following the experimental stroke operation, it was observed that rats administered QSW pretreatment had improved neurological function, reduced infarct volume (P < 0.01), increased Nissl bodies (P < 0.05), improved histopathology, and reduced BBB disruption. Immunofluorescence, RT-qPCR, and WB results showed that MMP-9 level in the brain tissue of the QSW pretreatment group had a decreasing trend and the expression of claudin-5 and occludin had a tendency to increase. Eleven metabolites related to lipid metabolism, fatty acid metabolism, and energy metabolism, were identified via GC–MS metabonomics. Our study shows that QSW preconditioning has a neuroprotective effect on CI/RI; however, its mechanism requires further study.