Recent studies have demonstrated that hemodialysis patients exhibit disruptions in functional networks with invisible cerebral alterations. We explored the alterations of functional connectivity in hemodialysis patients using the graph-theory method. A total of 46 hemodialysis patients (53.11 +/- 1.58 years, 28 males) and 47 healthy controls (55.57 +/- 0.86 years, 22 males) were scanned by using resting-state functional magnetic resonance imaging. The brains of these patients were divided into 90 regions and functional connectivity was constructed with the automatic anatomical labeling atlas. In the defined threshold range, the graph-theory analysis was performed to compare the topological properties including global, regional and edge parameters between the hemodialysis and the healthy control groups. Both hemodialysis patients and healthy control subjects demonstrated common small-world property of the brain functional connections. At the global level, the parameters normalized clustering coefficients and small-worldness were significantly decreased in hemodialysis patients compared with those noted in healthy controls. At the regional level, abnormal nodal metrics (increased or decreased nodal degree, betweenness centrality and efficiency) were widely found in hemodialysis patients compared with those of healthy controls. The network-based statistical method was employed and two disrupted neural circuits with 18 nodes and 19 edges (P = 0.0139, corrected) and 10 nodes and 11 edges (P = 0.0399, corrected) were detected. Of note, the edge-increased functional connectivity was associated with the salience network and the frontal-temporal-basal ganglia connection, whereas the edge-decreased functional connectivity was associated with the frontoparietal network. The graph-theory method may be one of the potential tools to detect disruptions of cerebral functional connectivity and provide important evidence for understanding the neuropathology of hemodialysis patients from the disrupted network organization perspective.