Healthy aging not only benefits every individual, it is also useful to meet the challenge of the upcoming aging society. This requires mechanistic studies of how aging occurs. Mitochondria are the most important organelle for energy production, free radical metabolism and programmed cell death. Damaged and dysfunctional mitochondria are selectively removed by a mechanism of mitochondrial autophagy or mitophagy to protect the cells from excessive oxidative stress. The defective mitochondrial quality control may be closely link with aging. Caloric restriction and physical exercise stimulate both general autophagy and selective mitophagy. These will improve mitochondrial function and hugely benefit healthy aging.