Abnormal brain structural connectivity of end-stage renal disease(ESRD) is associated with cognitive impairment. However, the characteristics of cortical structural connectivity have not been investigated in ESRD patients. Here, we study structural connectivity of the entire cerebral cortex using a fiber connectivity density(FiCD) mapping method derived from diffusion tensor imaging(DTI) data of 25 ESRD patients and 20 healthy controls, and between-group differences were compared in a vertexwise manner. We also investigated the associations between these abnormal cortical connectivities and the clinical variables using Pearson correlation analysis and multifactor linear regression analysis. Our results demonstrated that the mean global FiCD value was significantly decreased in ESRD patients. Notably, FiCD values were significantly changed(decreased or increased) in certain cortical regions, which mainly involved the bilateral dorsolateral prefrontal cortex(DLPFC), inferior parietal cortex, lateral temporal cortex and middle occipital cortex. In ESRD patients, we found a trend of negative correlation between the increased FiCD values of bilateral middle frontal gyrus and serum creatinine, urea, parathyroid hormone(PTH) levels and dialysis duration. Only the white matter hyperintensity(WMH) scores were significantly negatively correlated with the global FiCD value in multifactor regression analysis. Our results suggested that ESRD patients exhibited extensive impaired cortical structural connectivity, which was related to the severity of WMHs. A compensation mechanism of cortical structural recombination may play a role in how the brain adapts to maintain optimal network function. Additionally, the serum creatinine, urea and PTH levels may be risk factors for brain structural network decompensation in ESRD patients.