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Purpose: To investigate the topology of the brain functional connectome and its abnormalities in relation to disease severity in patients with Parkinsons disease (PD). Methods: One hundred and fifty-three PD patients and 81 healthy controls (HC) were recruited to undergo a resting-state functional magnetic resonance imaging. Functional connectivity between 90 brain regions from the automated anatomical labeling atlas was established using partial correlation coefficients, and the whole-brain functional connectome was constructed by applying a threshold to the resultant 90×90 partial correlation matrix. Graph theory analysis was then used to examine the group-specific topological properties of the two functional connectomes. After significant between-group differences had been identified in the network metrics, we correlated these metrics with the Unified PD Rating Scale (UPDRS)-Ⅲ scores in the PD group, using age and gender as covariates, and assessed their relationship to Hoehn and Yahr stage using a one-way analysis of variance. Results: Both the PD and HC groups exhibited “small-world” brain network topology. However, the functional connectome of the PD group showed a significant decrease in the global and local efficiency and clustering coefficient, and increase in characteristic path length. The PD showed reduced nodal centralities in the sensorimotor cortex, temporal-occipital regions and default mode network (DMN). Furthermore, the decline in the nodal centralities with disease progression were restricted to right precentral gyrus, left postcentral gyrus and left superior temporal gyrus, which were all connected with key regions in the DMN, including left angular gyrus, left superior frontal gyrus and right posterior cingulate gyrus. Finally, UPDRS-Ⅲ score was negatively correlated with nodal degree of the left postcentral gyrus and left superior temporal gyrus. Conclusion: The configurations of brain functional networks in PD patients were perturbed, notably those responsible for motor and cognition. These results give insights into understanding the topological aspects of the neuropathophysiology of PD. Further validation of the Hoehn and Yahr stage-related signal changes trend could potentially lead to development of a new biomarker of disease progression in PD.