We investigated the functional neural organization of the motor cerebro-cerebellar system in Parkinson’s disease (PD) patients with tremor-dominant (TD) or postural instability and gait disorder (PIGD) variant. A seed-cerebellar region (lobule VI of cerebellum) was defined based on motor task-based functional MRI in healthy controls. Functional connectivity was found to be disrupted in both PD subgroups between cerebellum, thalamus and default-mode regions. We identified different localization of functional over‐connectivity, PD-PIGD within inferior frontal gyrus and insula, while PD-TD in orbitofrontal gyrus. This study might provide novel insight into the underlying pathophysiological mechanism in PD subtypes.