Patients with Parkinson's disease have great difficulty in performing bimanual movements; this problem is more obvious when they perform bimanual anti-phase movements. The underlying mechanism of this problem remains unclear. In the current study, we used functional magnetic resonance imaging to study the bimanual coordination associated changes of brain activity and inter-regional interactions in Parkinson's disease. Subjects were asked to perform right-handed, bimanual in-phase and bimanual anti-phase movements. After practice, normal subjects performed all tasks correctly. Patients with Parkinson's disease performed in-phase movements correctly. However, some patients still made infrequent errors during anti-phase movements; they tended to revert to in-phase movement. Functional magnetic resonance imaging results showed that the supplementary motor area was more activated during anti-phase movement than in-phase movement in controls, but not in patients. In performing anti-phase movements, patients with Parkinson's disease showed less activity in the basal ganglia and supplementary motor area, and had more activation in the primary motor cortex, premotor cortex, inferior frontal gyrus, precuneus and cerebellum compared with normal subjects. The basal ganglia and dorsolateral prefrontal cortex were less connected with the supplementary motor area, whereas the primary motor cortex, parietal cortex, precuneus and cerebellum were more strongly connected with the supplementary motor area in patients with Parkinson's disease than in controls. Our findings suggest that dysfunction of the supplementary motor area and basal ganglia, abnormal interactions of brain networks and disrupted attentional networks are probably important reasons contributing to the difficulty of the patients in performing bimanual anti-phase movements. The patients require more brain activity and stronger connectivity in some brain regions to compensate for dysfunction of the supplementary motor area and basal ganglia in order to perform bimanual movements correctly.