Objective  To observe cognitive function and changes in neuroimaging markers in patients with chronic kidney disease (CKD) before and after initiation of hemodialysis (HD), and to analyze the relationship between them. Methods  A prospective cohort study was conducted in 40 patients with stage 5 CKD. Laboratory tests, cognitive function assessment using the Montreal Cognitive Assessment (MoCA) scale, and brain magnetic resonance imaging (MRI) were performed before HD initiation and after 1 year of HD. Arterial spin labeling (ASL) and quantitative susceptibility mapping (QSM) were used to assess the cerebral blood flow (CBF) and susceptibility values in brain regions including the bilateral hippocampus, thalamus, caudate nucleus, and putamen. Changes in clinical indicators, cognitive function, as well as CBF, susceptibility values, and CBF- susceptibility coupling in the above-mentioned regions of interest before and after HD initiation were analyzed, and the relationship between cognitive function and CBF-susceptibility coupling was also explored. Results  32 patients completed the cohort follow-up of the study. After one year of HD treatment, cognitive function was significantly improved compared with t baseline (Z=-3.266, P＜0.001). Compared with the baseline, the CBF in the bilateral hippocampus and right thalamus decreased, while the CBF in the right caudate nucleus increased (t=2.192, P=0.036; Z=2.616, P=0.009; t=2.488, P=0.018; Z=-2.460, P=0.020); the susceptibility values in the bilateral hippocampus increased, and those in the bilateral caudate nucleus and bilateral putamen decreased (Z=-3.983, P＜0.001; Z=-3.833, P＜0.001; t=4.352, P＜0.001; t=2.165, P=0.038; t=3.810, P=0.001; Z=3.665, P＜0.001). More importantly, the CBF-susceptibility coupling in the bilateral hippocampus was significantly increased (Z=-3.646, P＜0.001; Z=-4.600, P＜0.001), and the improvement in cognitive function was correlated with an increase of CBF-susceptibility coupling in the right hippocampus (r=0.431, P=0.014).  Conclusion   After one year of HD, the changes in CBF, susceptibility values, and CBF-susceptibility coupling in some brain regions of CKD patients are partially reversed, which was associated with the improvement in cognitive function.