Stem cells are the special cells which play a key role in the whole life cycle. It is very important to maintain the activity of stem cells, slow down stem cell aging and prolong the life of stem cells. In this paper, the molecular mechanism of stem cell aging is reviewed from the aspects including genome maintenance, telomeres, cell cycle inhibitors and mitochondria. The relationship between telomere-p53 pathway and mitochondria-reactive oxygen species pathway is focused, and the impacts of the two pathways on stem cell aging are introduced.