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It is unclear how the brain network changed after kidney transplantation (KT). We explored the patterns of large‐scale complex network after KT in end‐stage renal disease (ESRD) patients with resting‐state functional MRI (rs‐fMRI) and diffusion tensor imaging (DTI). Twenty‐one ESRD patients (14 men; mean age, 31.5 ± 9.9 years) scheduled for KT and 17 age‐ and gender‐matched healthy controls (HC) (8 men; mean age, 28.9 ± 7.2 years) were enrolled in this study. Each participant underwent rs‐fMRI and DTI scans in three time points (pre‐KT, 1 and 6 months after KT [for ESRD]). Graph theory analysis was used to characterize the topological properties by using functional and structural network connectivities intergroup correlation analysis was performed between functional/structural MR indexes and clinical markers. Compared with HC, pre‐KT ESRD patients showed an altered topological organization in both functional and structural networks. Compared with pre‐KT, increased node degree and node efficiency were observed for both functional and structural networks at 1 month after KT (all p <.05), which were further increased at 6 months after KT (p <.05). Both functional and structural networks did not recover completely at 6 months after KT (all p <.05). The patients showed an increased functional–structural connectivity coupling at 1 month after KT compared with HC (p =.041). A trend of progressive recovery of functional and structural connectivity networks was observed in ERSD patients after KT, which did not recover to the normal levels even in 6 months after KT. The study results underlie cognitive function recovery in ESRD patients following KT in the neuropathophysiological perspective. [ABSTRACT FROM AUTHOR]