In this paper, the aging of the stem cells has been elucidated in the aspect of quantitative and qualitative exhaustion, such as balance self-renewal and differentiation of hematopoietic stem cells. The reduced telomere and oxidative stress both accelerate the aging course, besides, histone code and transcriptional activation lead to the DNA or protein damage. It plays an important role in the stem cell aging that the modulation of allochromosome structure and epigenetic regulation of gene transcription. If the aging of the stem cells doesn’t happen on the level of the gene, it must result from the transcription. During the haemopoiesis process of stem cells, all kinds of the transcriptional mistakes will lead to the aging of cell cycle, which is the result of allochromosome enlarging. However, the above mechanism will not occur normally. Only allochromosome allotopia is not explainable to the gene expression of stem cells. The proof of stem cells’ self-renewal evidences that if not the consequence of cell expression, allochromosome change the histone.