Mitochondria are important organelles of eukaryotic cells and confer regulatory roles in energy conversion, cellular stress, lipid synthesis, and cell death. A plethora of mitochondrial proteases are involved in protein transport, processing activation and degradation. Among them, adenosine triphosphate ATP-dependent mitochondrial proteases, based on ATP hydrolysis through their Adenosine triphosphatases (ATPases) associated with diverse cellular activities (AAA+) structural domain, the quality control of mitochondrial protein and regulate protein degradation. Alterations in mitochondrial protease activity can lead to mitochondrial dysfunction, thus leading to a variety of human disease, including cardiovascular disease (CVDs), neurodegenerative disease, aging, and tumor. This study provides a systematic review of several well-studied ATP-dependent mitochondrial proteases and explores their functional relevance and clinical implications to human disease.