Voxel-based morphometry can be used to quantitatively compare structural differences and functional changes of gray matter in subjects. In the present study, we compared gray matter images of 32 patients with Parkinson's disease and 25 healthy controls using voxel-based morphometry based on 3.0 T high-field magnetic resonance T1-weighted imaging and clinical neurological scale scores. Results showed that the scores in Mini-Mental State Examination and Montreal Cognitive Assessment were lower in patients compared with controls. In particular, the scores of visuospatial/executive function items in Montreal Cognitive Assessment were significantly reduced, but mean scores of non-motor symptoms significantly increased, in patients with Parkinson's disease. In dition, gray matter volume was significantly diminished in Parkinson's disease patients compared with normal controls, including bilateral temporal lobe, bilateral occipital lobe, bilateral parietal lobe, bilateral frontal lobe, bilateral insular lobe, bilateral parahippocampal gyrus, bilateral amygdale, right uncus, and right posterior lobe of the cerebellum. These findings indicate that voxel-based phometry can accurately and quantitatively assess the loss of gray matter volume in patients with Parkinson's disease, and provide essential neuroimaging evidence for multisystem pathological mechanisms involved in Parkinson's disease.