Objective：This study aims to explore the effect of quantitative susceptibility mapping（QSM）in evaluating brain iron deposition in the patients with end-stage renal disease（ESRD）and the impact of iron deposition on cognitive function by comparing the magnetic susceptibility value（MSV）of the deep gray matter nuclei between the patients with ESRD and healthy controls，and analyzed the correlations between the MSVs of the patients with ESRD and the scores of the Montreal Cognitive Assessment（MoCA）. Methods：Twenty-five patients with ESRD and 25 healthy controls who are age and sex-matched were recruited in this study. The MSVs of the deep gray matter nuclei of all the patients with ESRD and healthy controls were measured with QSM. The differences of the MSVs of the nuclei between the patients and controls were analyzed by the Mann-Whitney U test. The diagnostic efficacy of the MSVs was analyzed by the receiver operating characteristic（ROC）curve. The correlations between the MSVs of the patients and the scores of the MoCA were analyzed by Spearman correlation analysis. Results：In the patients with ESRD，the MSVs of bilateral red nucleus（RN），substantia nigra（SN），caudate head（CA）and putamen（PU） were higher than those in the controls（P＜0.05 respectively）. The MSVs of bilateral RN，SN，PU and CA can distinguish the patients from healthy controls. ROC analysis revealed that the cut-off values of PU MSV（0.085） provided the best combination of sensitivity（67%） and specificity（91%） to distinguish the ESRD patients from controls. In the patients with ESRD，the MSV of the right RN was negatively correlated with language ability and abstract ability，the left CA was negatively correlated with attention and language ability，and the left globus pallidus（GP） was negatively correlated with visuospatial and executive ability（P＜0.05 respectively）. Conclusion：In patients with ESRD，QSM not only can evaluate brain iron deposition quantitatively，but contribute to analyze the impact of iron deposition on cognitive function.