The changes of whole brain functional connectivity in hemodialysis (HD) patients with end-stage renal disease (ESRD) are still unclear, which may be associated with multiple factors, such as elevated neurotoxins, anemia, and side effects of hemodialysis. Resting-state functional magnetic resonance imaging (rs-fMRI) data of 71 patients (43 males, 28 females; mean age, 33.4 ± 9.4 years) and 43 age- and gender-matched healthy volunteers (29 males, 14 females; mean age, 30.6 ± 8.8 years) were acquired. Neuropsychological tests including number connection test type A (NCT-A), digit symbol test (DST), line-tracing test (LTT), serial-dotting test (SDT), self-rating depression scale (SDS) and self-rating anxiety scale (SAS) were used to evaluate cognitive and psychiatric conditions in all subjects. Blood biochemistry tests including serum creatinine levels, blood urea, hematocrit, and Ca(2+) level were taken in HD patients. Forty-two connections significantly different between HD patients with ESRD and controls were found (all P < 0.05, Bonferroni corrected) and identified as connectivities of interests (COIs), among which 39 connections (92.9%) were markedly decreased in patients. Of the 39 weaker connections, 24 were related to the frontal lobe regions. Widespread weakening of cortical and subcortical network connectivity in ESRD patients was more directly related with neuropsychological impairments and anemia rather than serum creatinine level, blood urea and dialysis duration. In particular, impairments in the medial prefrontal lobe could play an important role in mediating psychological dysfunctions.