The relationship between intestinal flora and diseases is currently a hot topic of research, but most studies tend to explain causality and pathogenesis, and there is still a lack of studies of the traditional Chinese medicine (TCM) characteristics of intestinal microecological disorders from the perspective of etiology. The TCM pathogenic characteristics of hybrid flora need to be further clarified. The intestinal flora is an important bridge between the internal and the external environment of body, and plays an important and complex role in the diagnosis, prognosis, and treatment of diseases. Based on the etiology theory of TCM, this paper discusses the scientific connotation of changes of wind, fire, dryness, dampness, and cold caused by intestinal microecological disorder from the aspects of basic concepts, formation causes, and pathogenic nature and characteristics, combined with the nervous system, immune system, gland secretion, and nutritional metabolism, based on clinical manifestations, using the method of examining symptoms and seeking causes. This paper provides a new idea for the study of intestinal flora in TCM, and supplements and enriches the theory of etiology. At the same time, it provides an innovative theoretical basis for the understanding and research that intestinal microecological disorders can promote the occurrence and development of various complex diseases.