The mitochondrion is the site of energy metabolism inside the cell; which produces ATP for vital activities. The accumulation of damaged mitochondria affects cell survival, these organelles are removed via mitophagy to maintain cell vitality. Currently, mitophagy is a hot topic in life science research. Understanding the role of mitophagy in pathogenesis and its association with the genesis of disease is important for developing treatments for many human diseases. Here, we summarize current progress in the study of mitophagy and describe the different molecular mechanisms of mitophagy between yeast and mammals, as well as related diseases.