Iodine is an essential trace element in the human body, and the gastrointestinal tract is the main way for the body to intake iodine. The intestinal tract contains trillions of microorganisms that have important impacts on the substance-energy metabolism and the genetic information processing in the human body. Gut microbiota or their metabolites can act on the thyroid through the circulatory system (namely the " gut-thyroid axis" ), thus potentially regulating iodine metabolism in thyroid. This article reviews the effects of gut microbiota on intestinal iodine uptake, as well as the effects of gut microbiota and their metabolites on the expression and activity of sodium iodide symporter (NIS) in thyroid cells, thus exploring the potential regulatory mechanisms of gut microbiota that involved in thyroid iodine metabolism. Potential factors affecting thyroid iodine metabolism by gut microbiota include the direct and the indirect factors. The direct factors include lipopolysaccharides, short-chain fatty acids, microbial peptides, and microbial proteins, which may affect the expression or activity of NIS in thyroid by regulating the nuclear factor kappa-B pathway, histone acetylation modifications, or antigen-antibody reactions. The indirect factors include the altered cellular environment that effected by gut microbiota which can further affect the transport of iodine ions in thyroid cells by manners like regulating the levels of thyroid-specific transcription factors and regulating the signal pathways mediated by thyroid-stimulating hormone and its receptor.