In the long-term evolution, microbes and hosts coexist widely, forming a symbiotic microecosystem and resulting the complex interactions of the metabolism. With the application of microecological theory in Chinese materia medica science, two main points have been accepted gradually. On the one hand, the prevention and treatment of human diseases by traditional Chinese medicines can be achieved through the correction and adjustment of the imbalance of the human microecosystem. On the other hand, the microecosystem can regulate the quality of traditional Chinese medicines in real time, and further affect their curative effect. Thus, a new discipline, Traditional Chinese Medical Microecology, has been gradually established. In this review, the background, theoretical structure, research directions, key problems and the relationship with human microecology of Traditional Chinese Medical Microecology were systematically summarized and prospected for promoting its development. Moreover, this review provides a reference protocol for further discoursing the microecological mechanism involving the efficacy of traditional Chinese medicines.