With the rise of microecology and medical model getting into the stage of the development of the ecological medicine, the intersection and consistency in the cognition traditional of Chinese and Western medical system are highlighted. Yin-yang theory is the core theory in TCM. In order to extend the guidance effects of theory of the balance of yin and yang in the clinic, and help TCM theory and curative effect be further recognized by the world, this article analyzed the consistency of different systems by comparing TCM balance theory and microecology, with a purpose to explore the closed link between TCM balance theory and microecology and microscopic nature of TCM balance theory.