With the increasingly serious environmental pollution, studies on the toxicological mechanisms of environmental pollutants leading to health risks has caused great concerns. However, the investigation on how environmental pollutants affect the structure and function of the gut microbiota and its regulation of toxic effects is still largely unknown. Based on the characteristics of gut microbiota in the human and animal models, this paper focused on the structure, diversity and composition of gut microbiota altered by typical environmental pollutants including heavy metals, micro-nano particle, persistent organic pollutants and antibiotics. In addition, the potential regulatory role of gut microbiota in the toxicological effects of organisms were summarized. It provided a theoretical basis for subsequent systematic studies on gut microbiota regulated toxicological effects of environmental pollutants and human health risks.