Abstract: Hemodialysis is one of the important ways to prolong the life of patients with end-stage renal disease, but its mortality rate is significantly higher than that of normal people. Cerebrovascular accident, congestive heart failure and pulmonary infection are the most common causes of death in hemodialysis patients in China. The gut microbiota is involved in a complex network of human organs and closely related to many diseases of human systems. The gut microbiota specific to hemodialysis patients and their metabolites-induced gut-heart axis, gut-brain axis and gut-lung axis play an important role in cardiovascular, cerebrovascular and respiratory diseases. All are associated with all-cause mortality in hemodialysis patients. In this review, we focused on describing how gut microbiota and the metabolites in hemodialysis patients affect the occurrence and development of high-risk comorbidities like heart failure, stroke and respiratory tract infection. The results showed that changes in the gut microbiota structure, reduced production of short-chain fatty acids and increased intestinal protein-binding toxins in hemodialysis patients may increase the susceptibility to these diseases, accelerate disease progression and worsen the prognosis.