Stroke is the second most common cause of death after cancer worldwide and a major cause of acquired disability in adults. Overwhelming majority of strokes are caused by cerebral ischemia and are classified as ischemic stroke. Microglia are the resident immune cells and play dual roles in response to ischemia injury in the central nervous system (CNS). On the one hand, microglia may contribute to tissue function recovery process by promoting inflammation resolution, cellular debris clearance, nerve regeneration and synapse remodeling. On the other hand, excessive activation of microglia aggravates nerve damage after ischemic injury. Here, we briefly describe the mechanism of microglia activation after stroke, and comprehensively review the dual role of microglia in neurodegeneration and regeneration after stroke. In-depth exploration of the cytotoxic and protective mechanisms of microglia will provide new targets and new strategies for stroke treatment.