Abstract Introduction Xingnao Jiutan tablets (XNJT), a compound Chinese medicine, have been applied to the treatment of the sequelae of cerebral thrombosis or cerebral hemorrhage, transient cerebral ischemia, and central retinal vein obstruction, etc., but the underlying mechanisms are not yet clear. This research focused on examining the impact of XNJT for cerebral ischemia/reperfusion (MCAO/R) injury, utilizing gut microbiota and metabolomic studies. Methods The primary components of XNJT were identified through the application of the HPLC technique. We established a MCAO/ R model in mice and conducted behavioral evaluations, cerebral blood flow measurements, and TTC staining. We used ELISA, high-throughput 16S rDNA gene sequencing, and metabolomics techniques to detect inflammatory factors, microbial populations, and metabolites, respectively. Finally, we performed Spearman correlation analysis to investigate the relationships among gut microbiota and metabolites, comprehensively exploring the mechanisms of XNJT to alleviate cerebral ischemia-reperfusion injury. Results We discovered that XNJT effectively enhanced neurological performance, alleviated cerebral infarction, diminished neuronal cell death, and increased cerebral blood flow. Moreover, XNJT downregulated the secretion of pro-inflammatory cytokines like TNF, IL-6, and IL-1b. Additionally, XNJT improved gut microbiota levels in MCAO/R mice, particularly Bacteroides, Firmicutes, Escherichia-Shigella, and Ligilactobacillus. Furthermore, XNJT primarily modulated differential metabolites in the gut through Glycerophospholipid, Linoleic acid, and Sphingolipid metabolism pathways. Spearman correlation analysis revealed significant associations among intestinal microbiota and various metabolites. Discussion In summary, our findings suggest that XNJT can improve cerebral ischemia/reperfusion injury outcomes, reduce inflammatory responses, and regulate gut microbiota and differential metabolites. It’s possible that the potential mechanisms are connected to controlling gut microbiota and metabolism. Keywords: Xingnao Jiutan tablets, cerebral ischemia/reperfusion, gut microbiota, metabolism, brain-gut axis 1. Introduction Stroke, a disorder of the central nervous system, is marked by high morbidity, mortality, disability, and economic burden due to brain tissue damage from blocked or burst blood vessels in the brain ([39]Grysiewicz et al., 2008). Research indicates that worldwide, stroke ranks as the second most common cause of mortality, representing 11.6% of total deaths, and is the third leading reason for disability ([40]Demsie and Lorkowski, 2020; [41]Feigin et al., 2022). Additionally, China has the highest stroke prevalence worldwide, with a trend toward younger patients ([42]Zhou et al., 2019; [43]Xian et al., 2022). Stroke types include ischemic stroke and cerebral hemorrhagic stroke, where ischemic stroke occurs more frequently, constituting 60% to 80% of all stroke cases ([44]Herpich and Rincon, 2020; [45]Liu et al., 2020). The primary cause of ischemic stroke is the blockage of the intracranial artery, leading to intricate brain neuropathological alterations such as excitotoxicity, oxidative stress, neuroinflammation, and breakdown of the blood-brain barrier, culminating in brain tissue death and neurological impairments ([46]Maida et al., 2020; [47]Candelario-Jalil et al., 2022; [48]Huang et al., 2022; [49]Rajeev et al., 2022; [50]Zong et al., 2022). Clinical manifestations of neurological deficits include hemiparesis, speech difficulties, facial asymmetry, and impaired consciousness. Presently, thrombolysis and interventional treatment stand as the most efficacious therapies, yet they come with high costs and constraints like a limited time frame and related risks. Therefore, it’s critically important to develop efficient and economical treatment methods to reduce the burden of strokes on both society and families. In conclusion, studying the pathophysiologic process of ischemic stroke and establishing a comprehensive system for its prevention, diagnosis, treatment, and prognosis is of great significance. A growing collection of studies suggests that ischemic stroke affects gut microbiota and that regulating gut flora could be an innovative approach to preventing and treating strokes ([51]Pluta et al., 2021; [52]Yamashiro et al., 2021; [53]Zhang et al., 2021). Dysbiosis of the gut microbiota can disrupt brain function and result in neurological disorders ([54]Durgan et al., 2019). Furthermore, gut microbiota-related metabolites, including short-chain fatty acids and lipopolysaccharides, show a significant correlation with the development and outcomes of stroke ([55]Chen et al., 2019b; [56]Cheng et al., 2022). This suggests a role for the brain-microbe-gut axis in the pathology of strokes. Gut microbiota serves as a “two-way” communication system between the gastrointestinal system and the brain. Recently, the healing impact of Chinese medicine on a range of illnesses has gained broad acknowledgment, along with its recognized