The gut microbiome affects the enterohepatic recycling of thyroid hormone and the metabolism and absorption of micronutrients including iodine and selenium. Changes in thyroid function trigger changes in the neuro-muscular function of the gut, resulting in a two-way interaction that affects the composition of gut microbiome. In recent years, based on animal experiments and prospective clinical studies, many possibilities have been suggested that the influences in naïve immune cells differentiation or increasing permeability of proinflammatory cytokines and endotoxins to blood due to intestinal integrity disruption may affect the progression of autoimmune thyroid disease or thyroid cancers. In this review, we focused on refining the progression on the hypothesis that there is a link between the gut microbiome and the thyroid gland.