Objective To explore the damage of cerebral cortex in patients with hepatolenticular degeneration (HLD). Methods Twenty four patients with HLD and 27 healthy volunteers were enrolled in this study. The left and right globus pallidus were selected as ROI, the whole brain functional connectivity was calculated. The brain functional connectivity between patients with HLD and healthy volunteers was compared. Results Compared with healthy volunteers, the functional connections of patients with HLD between the left globus pallidus and the brain stem and bilateral thalamus were decreased, while the functional connections between the right globus pallidus and several brain regions were decreased, including bilateral thalamus, bilateral middle frontal gyrus (MFG), bilateral insula, left anterior cingulate gyrus (ACC), left middle cingulate gyrus (MCC), brainstem and left cerebellum. Conclusion The results show that the abnormal connectivity of globus pallidus is widely distributed in HLD group, including cerebellar thalamic cortical circuit, motor, emotional and cognitive networks such as salience network and Communist Youth Network, which may be an important factor leading to clinical symptoms of HLD patients.