End-stage renal disease (ESRD) is associated with vascular and neuronal dysfunction, causing neurovascular coupling (NVC) dysfunction, but how NVC dysfunction acts on the mechanism of cognitive impairment in ESRD patients from local to remote is still poorly understood. We recruited 48 ESRD patients and 35 demographically matched healthy controls to scan resting-state functional MRI and arterial spin labeling, then investigated the four types of NVC between amplitude of low-frequency fluctuation (ALFF), fractional ALFF, regional homogeneity, degree centrality, and cerebral blood perfusion (CBF), and associated functional networks. Our results indicated that ESRD patients showed NVC dysfunction in global gray matter and multiple brain regions due to the mismatch between CBF and neural activity, and associated disrupted functional connectivity (FC) within sensorimotor network (SMN), visual network (VN), default mode network (DMN), salience network (SN), and disrupted FC between them with limbic network (LN), while increased FC between SMN and DMN. Anemia may affect the NVC of middle occipital gyrus and precuneus, and increased pulse pressure may result in disrupted FC with SMN. The NVC dysfunction of the right precuneus, middle frontal gyrus, and parahippocampal gyrus and the FC between the right angular gyrus and the right anterior cingulate gyrus may reflect cognitive impairment in ESRD patients. Our study confirmed that ESRD patients may exist NVC dysfunction and disrupted functional integration in SMN, VN, DMN, SN and LN, serving as one of the mechanisms of cognitive impairment. Anemia and increased pulse pressure may be related risk factors.