In recent years the interaction between host and gut microbiota has attracted increasing attention. However, intestinal flora dysbiosis may lead to many diseases, and there is increasing evidence that the intestinal microbiota in patients with chronic kidney disease (CKD) is associated with the pathophysiological status of the host. "Gut-kidney axis" provides a better explanation of the two-way communication between intestinal flora and CKD. Impaired kidney function leads to dysbiosis of intestinal flora and an altered intestinal flora can damage the intestinal mucosal barrier and facilitate the entry into the bloodstream of harmful bacteria, which can induce chronic inflammation and thus accelerate renal injury. In addition, the accumulation of nephrotoxic metabolites from an altered intestinal flora can aggravate CKD in the "gut-kidney axis". Among them, p-cresol sulfate, indoxyl sulfate and trimethylamine oxide are the most widely studied metabolites of nephrotoxicity, and their renal toxicity has been widely confirmed in basic research and clinical studies. Current studies show that the intestinal microbiota-metabolite network is closely related to the occurrence and development of chronic kidney disease. Thus, intervention in the intestinal microbiota may provide a new approach to the prevention and treatment of chronic kidney disease.