This study aimed to evaluate changes in gray matter nuclei iron deposition in chronic kidney disease (CKD) patients using the quantitative susceptibility mapping (QSM) threshold method, and analyze the relationship between brain iron levels and cognitive function. A total of fifty-three CKD patients were prospectively recruited, comprising 35 hemodialysis (HD, 57.54 ± 10.42 years, 21 males) and 18 non-hemodialysis (NHD, 55.06 ± 11.47 years, 10 males ), and were compared to 43 healthy controls (HC, 55.67 ± 7.79 years, 18 males). All participants underwent clinical assessments, neuropsychological tests, and QSM scans. The mean magnetic susceptibility value (MSV) and volume of the whole nuclei (MSV