Multiple Sclerosis (MS) is a chronic autoimmune disease of the central nervous system (CNS) characterized by neuroinflammation and neurodegeneration. The pathogenesis of these diseases is complex, and a variety of central nervous system and peripheral cells are involved. In recent years, single-cell sequencing has gradually been applied in neurological disorder, which is of great significance for understanding intercellular heterogeneity, disease development mechanisms, and treatment strategies. This review will summarize the single-cell sequencing and its applications in MS.