The present invention relates to a method using a cell penetrating peptide (Pep-1) for labeling and delivering mitochondria separated from healthy cells to replace damaged mitochondria. At present, microinjection of mitochondria into cells can only process one cell at a time, and therefore, this technique is limited to embryo related research and relevant applications. The advantages of the said peptide-mediated mitochondrial delivery system (PMD) include less steps with more efficiency, where a number of cells can be treated following one labeling process; the delivery process can be easily controlled, there is no cell toxicity after delivery under appropriate conditions, and delivery efficiency is over 80% depending on different cell types. Mitochondria delivered by the PMD system will move to the original mitochondrial location in the cells and will not be catalyzed in lysosomes; thus, the therapeutic effects can last at least one week.