Ischemic stroke is the third leading cause of death in the world. Our previous study found that cynandione A (CYNA), the main component from the root of Cynanchum bungei, exhibits anti-ischemic stroke activity. In this work, we investigated the therapeutic mechanisms of CYNA to ischemic stroke at protein network level. First, PC12 cells and cerebellar granule neurons were prepared to validate the effects of CYNA against glutamate injury. Our experiments suggested that CYNA could dose-dependently mitigate glutamate-induced neurons neurotoxicity and inhibit glutamate-induced upregulation of KHSRP and HMGB1, further confirming the neuroprotective effects of CYNA in vivo. Then, on the pathway sub-networks, which present biological processes that can be impacted directly or in periphery nodes by drugs via their targets, we found that CYNA regulates 11 pathways associated with the biological process of thrombotic or embolic occlusion of a cerebral artery. Meanwhile, by defining a network-based anti-ischemic stroke effect score, we showed that CYNA has a significantly higher effect score than random counterparts, which suggests a synergistic effect of CYNA to ischemic stroke. This study may shed new lights on the study of network based pharmacology.