The intestinal flora is composed of a large number of aerobic and anaerobic bacteria, viruses and other components, which involved in maintaining many physiological function of the body. It has a crucial link with the balance of digestion, absorption, immune, endocrine and metabolic absorption and digestion of nutrients, in order to make the body remained stable. The signal substance required for the association of intestinal flora with the organism may be part of the bacterial interaction or the metabolite produced by itself. When the intestinal flora disorder, the body may appear a series of diseases. It has a connection between the endocrine and immune related diseases such as type 1 diabetes, type 2 diabetes, and inflammation Enteritis, rheumatoid arthritis and intestinal flora disorder. As a important endocrine gland, it has a certain correlation between thyroid and the body hormone regulation which acts an important role in complex environment. There are many different kinds of thyroid diseases, the pathogenesis of symptoms are complex, at the same time the mechanism is not very clear, such as Graves's disease, Hashimoto's thyroiditis subacute thyroiditis, and so on. This article reviews the research progress of the relationship between the tyroid related diseases and disorders of the gut flora, in order to exploring the guiding significance of disease prevention, diagnosis and treatment.