Regulatory T cells (Tregs) can clear autoreactive lymphocytes, induce self-tolerance, and suppress inflammatory response. As the energy factories of cells, mitochondria are critical for the function, differentiation, and survival of Tregs. Studies have found Treg abnormalities and mitochondrial damage in patients with central nervous system autoimmune diseases, such as multiple sclerosis, neuromyelitis optica spectrum disorder, and autoimmune encephalitis. However, the role of mitochondrial-regulated Tregs in central nervous system autoimmune diseases remains inconclusive. Therefore, this review focuses on the effects of mitochondrial damage on Tregs in central nervous system autoimmune diseases and the possible mitochondrial therapeutic targets.