Microglia, as the resident immune cells and first responder to neurological insults, play an extremely important role in the pathophysiological process of spinal cord injury. On the one hand, microglia respond rapidly and gather around the lesion in the early stage of injury to exert a protective role, but with the continuous stimulation of the injury, the excessive activated microglia secrete a large number of harmful substances, aggravate the injury of spinal cord tissue, and affect functional recovery. The effects of microglia depletion on the repair of spinal cord injury remain unclear, and there is no uniformly accepted paradigm for the removal methods and timing of microglia depletion, but different microglia depletion strategies greatly affect the outcomes after spinal cord injury. Therefore, this review summarizes the physiological and pathological roles of microglia, especially the effects of microglia depletion on spinal cord injury—sustained microglial depletion would aggravate injury and impair functional recovery, while the short-term depletion of microglial population in diseased conditions seems to improve tissue repair and promote functional improvement after spinal cord injury. Furthermore, we discuss the advantages and disadvantages of major strategies and timing of microglia depletion to provide potential strategy for the treatment of spinal cord injury.