Skeletal muscle wasting refers to the loss of skeletal muscle mass and function. Mitochondrial quality control (MQC) is the basis for maintaining normal physiological mitochondrial function, which mainly involves the regulation of mitochondrial biogenesis, mitochondrial dynamics (fission/fusion) and mitophagy. It maintains muscle homeostasis by regulating the relative stability of mitochondrial shape, quantity and quality. As an economical and effective treatment for muscular atrophy, exercise intervention has been widely used, but the relationship between exercise intervention and MQC is not clear. This paper discusses the role of mitochondrial biogenesis, mitochondrial dynamics, and mitophagy in skeletal muscle atrophy and related molecular targets, and thoroughly analyzes the mechanism of MQC-mediated exercise in improving skeletal muscle atrophy caused by aging, disuse, and cancer cachexia, in order to provide theoretical guidance for exercise intervention in skeletal muscle atrophy.