The present invention provides a method for activating proliferation, migration and differentiation of stem cells in an animal comprising the preparation of the activating agent, the step of administering to the animal an effective amount of chlorine dioxide and the use of the chlorine dioxide for activating proliferation, migration and differentiation of stem cells. The method of the invention, with a wide application range, can be used in the treatments which need the tissue regeneration and immunomodulatory capability of stem cells and to the activation of proliferation, migration and differentiation of stem cells in injured organs and/or tissues. Besides, the method can act promptly, moderately and persistently in proliferation, migration and differentiation of stem cells, with few or no side effects.