Abstract Background: Clinical research found that Hedysarum Multijugum Maxim.-Chuanxiong Rhizoma Compound (HCC) has definite curative effect on cerebral ischemic diseases, such as ischemic stroke and cerebral ischemia-reperfusion injury (CIR). However, its mechanism for treating cerebral ischemia is still not fully explained. Methods: The traditional Chinese medicine related database were utilized to obtain the components of HCC. The Pharmmapper were used to predict HCC’s potential targets. The CIR genes were obtained from Genecards and OMIM and the protein-protein interaction (PPI) data of HCC’s targets and IS genes were obtained from String database. After that, the DAVID platform was applied for Gene Ontology (GO) enrichment analysis and pathway enrichment analysis. Finally, a series of animal experiments were carried out to further explore the mechanism of HCC intervention in CIR. Results: The prediction results of systematic pharmacology showed that HCC can regulate CIR-related targets (such as AKT1, MAPK1, CASP3, EGFR), biological processes (such as angiogenesis, neuronal axonal injury, blood coagulation, calcium homeostasis) and signaling pathways (such as HIF-1, VEGF, Ras, FoxO signaling). The experiments showed that HCC can improve the neurological deficit score, decrease the volume of cerebral infarction and up-regulate the expression of HIF-1α/VEGF and VEGFR protein and mRNA (p < 0.05). Conclusion: HCC may play a therapeutic role by regulating CIR-related targets, biological processes and signaling pathways found on this study. Keywords: hedysarum multijugum maxim-chuanxiong rhizoma compound, cerebral ischemia-reperfusion injury, Ischemic stroke, cerebral ischemia, HIF-VEGF pathway, systematic pharmacology, chinese medicine Introduction Cerebrovascular disease is a common disease in the clinic, which seriously endangers human health and life. As the population of aging increases, the morbidity, mortality and disability rate of cerebrovascular disease were increasing year by year ([38]Thomas, 1996; [39]Sacco and Rundek, 2012; [40]Liu et al., 2015). Among them, ischemic cerebrovascular disease accounts for a large proportion. The key to cerebral ischemia treatment is to quickly restore cerebral blood perfusion and maintain smooth blood flow ([41]Frizzell, 2005; [42]Behravan et al., 2014). However, the brain injury may be further aggravated after the restoration of blood flow perfusion, that is cerebral ischemia-reperfusion injury (CIR). Ischemia-reperfusion injury (IRI) refers to the pathological phenomenon that the degree of tissue damage is increased after the blood supply to the ischemic tissue is restored for a certain period of time ([43]Wu et al., 2018). The harm of CIR is huge. It involves many complicated links and factors, which has been the focus of scientists’ research for many years. With the deepening of the research, while looking for neuroprotective drugs, a variety of comprehensive intervention strategies for CIR such as mild hypothermia, atmospheric hyperbaric therapy and ischemic preconditioning and ischemic postconditioning were also proposed ([44]Lapi and Colantuoni, 2015; [45]Patel and McMullen, 2017; [46]Leech et al., 2019); the drugs include: N-methyl-D-aspartic acid (NMDA) receptor antagonist, Ca[2] + channel blocker, ICAM-1 antibody, CDP-choline, and so on ([47]Lapi and Colantuoni, 2015; [48]Patel and McMullen, 2017). At present, natural plant ingredients have been found to improve microcirculation barriers after CIR, and Chinese medicine formulations have gradually become a new direction for new drug development ([49]Wang et al., 2019). Hedysarum Multijugum Maxim.-Chuanxiong Rhizoma Compound (HCC) was first used by the First Affiliated Hospital of Hunan University of Chinese Medicine. Clinical research showed that HCC has definite curative effect on cerebral ischemic diseases (such as ischemic stroke and CIR), and its clinical effective rate is over 90% ([50]Ge, 2014). This Chinese medicine formula is composed of Hedysarum Multijugum Maxim. [Leguminosae; Astragali Radix (Huang Qi)], Ligusticum striatum DC. [Apiaceae; Chuanxiong Rhizoma (Chuan Xiong)], Pheretima Aspergillum (E.Perrier) [Megascolecidae; Pheretima (Di Long)], Bombyx Batryticatus [A desiccated body formed by the 4–5 instar larvae of Bombyx mori Linnaeus (family: Bombycidae) infected with white Beauveria bassiana (Bals.) Vuillant; (Jiang Can)], and can reduce serum tumor necrosis factor (TNF) -α and plasma thromboxane B2 (TXB2) levels and increase plasma 6-Keto-PGF1α ([51]He et al., 2002). Our previous research also found that HCC can protect neurons in the hippocampal CA[2] region by regulating Fpn expression to balance iron levels after cerebral ischemia. This suggests that imbalance of intracellular iron balance may be a new mechanism of cerebral ischemia ([52]Liao et al., 2015). However, the mechanism of HCC in treating cerebral ischemia is still not fully explained. Systematic pharmacology is an emerging discipline based on the intersection and integration of multidisciplinary technologies such as classic pharmacology, computer technology, bioinformatics, and network pharmacology, which systematically studies the interactions between drugs and the human body at multiple levels, including molecules, cells, organs, and networks ([53]Zeng et al., 2017; [54]Zeng and Yang, 2017; [55]Bao et al., 2019; [56]Yang et al., 2019a; [57]Yang et al., 2019b). Our previous research used systematic pharmacological strategies to reveal the mechanism of Chinese medicine formula in the treatment of complex diseases in the fields of oncology and cardiovascular ([58]Zeng et al., 2017; [59]Zeng and Yang, 2017; [60]Bao et al., 2019; [61]Yang et al., 2019a; [62]Yang et al., 2019b). Therefore, this study hopes to reveal the complex mechanism of HCC through a systematic pharmacology strategy (integrating network pharmacology experimental pharmacology). Materials and Methods HCC’s Compounds Collection The components of HCC were collected from the traditional Chinese Medicine (TCM) Database at Taiwan ([63]http://tcm.cmu.edu.tw/zh-tw/) ([64]Chen et al., 2014) and the Traditional Chinese Medicine Systems Pharmacology Database (TcmSPTM, [65]http://tcmspw.com/tcmsp.php) ([66]Ru et al., 2014). The components with oral bioavailability (OB) ≥ 30%, Caco-2 permeability > −0.4 and drug-likeness (DL) ≥ 0.18 were considered as the potential bioactive compounds of HCC ([67]Walters and Murcko, 2002; [68]Ano et al., 2004; [69]Hu et al., 2009; [70]Xu et al., 2012; [71]Ru et al., 2014). Meanwhile, since the application of biological models to predict HCC compounds has limitations ([72]Metodiewa et al., 1997), a large number of references were