To 1) investigate the morphological brain-tissue changes in patients with dialysis- and non-dialysis-dependent chronic kidney disease (CKD); 2) analyze the effects of CKD on whole-brain cortical thickness, cortical volume, surface area, and surface curvature; and 3) analyze the correlation of these changes with clinical and biochemical indices. This study included normal controls (NCs, n = 34) and patients with CKD who were divided into dialysis (dialysis-dependent chronic kidney disease [DD-CKD], n = 26) and non-dialysis (non-dialysis patients who underwent cranial magnetic resonance imaging scans [NDD-CKD], n = 26) groups. Cortical thickness, volume, surface area, and surface curvature in each group were calculated using FreeSurfer software. Brain morphological indicators with statistical differences were correlated with clinical and biochemical indicators. Patients with CKD exhibited a significant and widespread decrease in cortical thickness and volume compared with NCs. Among the brain regions associated with higher neural activity, patients with CKD exhibited more significant morphological changes in the paracentral gyrus, transverse temporal gyrus, and lateral occipital cortex than in other brain regions. Cortical thickness and volume in patients with CKD correlated with blood pressure, lipid, hemoglobin, creatinine, and urea nitrogen levels. The extent of brain atrophy was further increased in the DD-CKD group compared with that in the NDD-CKD group. Patients with CKD potentially exhibit a certain degree of structural brain-tissue imaging changes, with morphological changes more pronounced in patients with DD-CKD, suggesting that blood urea nitrogen and dialysis may be influential factors in brain morphological changes in patients with CKD.© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.