Inflammation plays a vital role in the pathophysiology of ischemic stroke. Resident microglia are the first to respond to inflammatory response in cerebral ischemia. Traditionally, Microglia are regard as an important contributor to inflammation to aggravate brain injury. However, Recent studies have found that activated microglia exert anti-inflammatory production against ischemic injury. Future therapies targeting microglia may not exclusively aim at suppressing microglia activation, but also at modulating microglia polarization at different stages of ischemic stroke. With lacking effective therapy strategies for stroke, considerable attention has been attracted by Chinese Traditional Medicine (TCM). Many studies have reported that TCM protects ischemic injury by inhibiting activation of microglia and promote the different polarization of microglia phenotypes. The effects of TCM in mediating microglia activation and polarization during cerebral ischemia need to be further studied.