The theory of kidney-brain axis has provided more information for the interpretation of brain damage in ESRD patients. However, the factor of dialysis was ignored in this theoretical system. We analyzed the cortical structural changes and cognitive changes from different dimensions and also analyzed their relationship in ESRD patients with and without hemodialysis. We found that both the patients with dialysis and the patients without dialysis showed decreased cortical thickness when compared with healthy people, while the patients without dialysis presented with a more extensive decreased cortical thickness when compared with patients with maintenance hemodialysis. The brain structural changes were correlated with the cognitive changes. Our results suggested that the hemodialysis might be a protective factor for the brain, but the protective effect of hemodialysis was limited.