Celiac disease is an autoimmune-mediated enteropathy caused by ingestion of gluten in genetically susceptible population. Accumulating evidence has shown that the second human genome, intestinal microbiota, plays an important role in the development of celiac disease. Compared with the healthy population, patients with celiac disease show higher diversity in intestinal microbiota, but more proinflammatory bacteria and less beneficial bacteria in the gut, paralleled by the altered function and metabolism of gut microbiota. However, it is unclear how this dysbiosis of microorganism occurs and whether this change promotes celiac disease. This review is aimed at summarizing current evidence on the relationship between the gut dysbiosis and celiac disease, thus contributing the prevention and treatment of this disorder by regulating microbiota.