Mitochondria are important organelles in mammalian cells. As the regulatory center of cell energy metabolism and cell death, mitochondrial dysfunction will lead to the occurrence and development of a variety of diseases. Mitochondrial function depends on the integrity and homeostasis of mitochondrial proteome. Therefore, mitochondrial protein quality control system is very important to maintain mitochondrial homeostasis and body health. When mitochondria and their protein quality control system are abnormal, it will directly damage mitochondria and lead to abnormal mitochondrial protein accumulation, resulting in intracellular environmental disorder and even cell dysfunction, which may affect the occurrence and development of atherosclerotic diseases. This paper reviews the role of mitochondria and its protein quality control system in the occurrence and development of atherosclerotic diseases, and looks forward to the future development prospects and challenges in this field, in order to providing scientific evidence for finding specific mitochondrial protein closely related to atherosclerotic diseases.