This study aimed to demonstrate the longitudinal changes of brain volume in hemodialysis, and the relationship between brain volume and cognitive function. Thirty-three hemodialysis patients and thirty healthy controls (HCs) were recruited to this study. All patients underwent MR examinations to evaluate baseline and follow-up brain volume. Compared to the HCs, patients showed decreased gray matter (GM) volume and white matter (WM) volume. Compared to baseline patients, follow-up patients showed decreased GM volume and WM volume. The decreased left caudate volume was positively correlated with reduced neuropsychological scores in patients. Brain atrophy occurred in hemodialysis patients, leading to neurocognitive impairment.