Due to the pivotal role of mitochondria in the generation of adenosine triphosphate (ATP) and the regulation of cellular homeostasis, mitochondrial dysfunction may exert a profound impact on various physiological systems, potentially precipitating a spectrum of distinct diseases. Consequently, research pertaining to mitochondrial therapeutics has assumed increasing significance, warranting heightened scrutiny. In recent years, the field of mitochondrial therapy has witnessed noteworthy advancements, with active exploration into diverse pharmacological agents aimed at ameliorating mitochondrial function. Elamipretide (SS-31), a novel synthetic mitochondrial-targeted antioxidant, has emerged as a promising candidate with extensive therapeutic potential. Its notable attributes encompass the mitigation of oxidative stress, the suppression of inflammatory processes, the maintenance of mitochondrial dynamics, and the prevention of cellular apoptosis. As such, SS-31 may emerge as a viable choice for the treatment of mitochondrial dysfunction-related ailments in the foreseeable future. This article extensively expounds upon the superiority of SS-31 over natural antioxidants and traditional mitochondrial-targeted antioxidants, delves into its mechanisms of modulating mitochondrial function, and comprehensively summarizes its applications in alleviating mitochondrial dysfunction-associated disorders. Furthermore, we offer a comprehensive outlook on the expansive prospects of SS-31′s future development and application.