Microglia, a type of neuroglia, has a variety of functions such as phagocytosis, clearance, antigen presentation, promotion of repairment of injury and secretion of extracellular signaling molecules, in which phagocytosis of microglia plays a crucial role in maintaining brain tissue, remodeling synapses, clearance of several aberrant proteins such as amyloid β in neurodegenerative diseases, and in neurodevelopment. This review briefly summarizes the phagocytic function of microglia with underlying regulatory mechanism in neurodevelopment and neurodegenerative diseases, aiming to provide a new thought for the therapy of neurodegenerative diseases.