Background Cognition impairment is well known in patients with chronic kidney disease (CKD). The relationship between brain structure and cognitive performance in CKD patients is still under investigation. The study aimed to quantitatively assess the relationship between brain structure and cognitive performance in patients with CKD. Methods We recruited 39 patients with CKD and 39 age‐ and sex‐matched control participants from a tertiary medical center. All participants underwent 3‐T MRI scan neuropsychological assessments, and renal function tests. FreeSurfer software was used for imaging processing and analysis, including measurement of cortical thickness and gray matter (GM) and white matter volumes. Results Compared with control subjects (73.1±7.5 years old), patients with CKD (76.4±8.4 years old) had significantly lower scores on the Mini‐Mental State Examination, and forward digit span test (P<.01). Patients with CKD had smaller cerebral GM volume, hippocampus, and decreased cortical thickness (P<.01) relative to the control group. Estimated glomerular filtration rate (eGFR) was correlated with cognitive performance, cortical thickness, GM volume, and hippocampal volume (P<.001). Linear regression analysis revealed that eGFR and GM volume were independently negatively associated with cognitive performance (P<.001), while eGFR and age were negatively associated with cortical thinning and GM volume after controlling for confounding factors. Conclusions This study demonstrated that impaired kidney function is associated not only with poor cognitive performance, but also with small cerebral GM volume and reduced cortical thickness.