Based on summing up the latest research progress of the interaction between molecular clock and mitochondrial quality under exercise and dietary change, this study proposes that intermittent fasting may promote health by regulating the molecular clock through mitophagy. The interaction between the molecular clock and the mitochondria dynamics can effectively avoid insulin resistance caused by high fat diet. In terms of sports, it has been elucidated that PGC-1α, Fis1 and HIF-1α can interact with BMAL1 in adipose tissue, liver and skeletal muscle, respectively, and exercise regulates the interaction of molecular clock and MQC through BMAL1-HIF-1α,CLOCK-mitophagy, and AMPK-SIRT1-PGC-1α. However, the mechanism of long-term chrono-aerobic/anaerobic exercise and/or different exercise intensities/modes combined with intermittent fasting to regulate the interaction effect of mitochondrial quality and rhythmic molecular clock needs further study. Mitophagy may be the important link in this process. Whether exercise ameliorates metabolic abnormalities induced by high fat diet through the interaction effect of molecular clock and mitochondrial dynamics remains to be explored.