The aim of this study was to explore the correlation between iron deposition (ID) and cerebral blood flow (CBF) in the deep gray matter structures of hemodialysis patients using susceptibility-weighted image mapping and arterial spin labeling. Both ID and CBF of the patients were increased compared with the healthy controls. ID in patients was positively correlated with CBF in the right putamen, while negatively correlated with CBF in the right thalamus. Abnormal calcium-phosphorus metabolism and triglyceride were shared independent factors for increased ID and CBF. Increased ID, rather than CBF, was a risk factor for neurocognitive impairment.