Multiple sclerosis (MS) is a chronic autoimmune disease of the central nervous system characterized by neuroinflammation and neurodegeneration. The pathogenesis of the disease is complex, and involves various central nervous system and peripheral cells. Single-cell sequencing has recently been increasingly applied in the study of neurological disorders, leading to important advances in our understanding of intercellular heterogeneity, disease development mechanisms, and treatment strategies. This review summarizes research progress in single-cell sequencing and its applications in MS.