Abstract Mitochondria, as the “energy factories” of cells, are vital for maintaining cell life and function. Mitochondria are highly mobile organelles within cells, constantly changing their morphology through fusion and fission processes to achieve dynamic transitions between interconnected network structures and fragmented states. This phenomenon is known as mitochondrial dynamics. Disorders in mitochondrial dynamics contribute to the onset of autoimmune conditions such as rheumatoid arthritis, multiple sclerosis, myasthenia gravis, and systemic lupus erythematosus, among others. This article aims to review the roles of mitochondrial dynamics disorders in autoimmune diseases and small molecule drugs targeting mitochondrial dynamic proteins, with the ultimate goal of aiding the development of new clinical treatments.