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The study aimed to compare the whole-brain gray matter volume (GMV) and white matter volume (WMV) difference between primary angle closure glaucoma (PACG) patients and health controls (HCs) using a voxel-based morphometry method. A total of 27 patients with PACG (17 males and 10 females) and 27 HCs (17 males and 10 females), closely matched for age and education, were enrolled in the study. All subjects underwent magnetic resonance imaging (MRI) scans. The MRI data were processed using SPM8 software in voxel-based morphometry 8 toolbox. The relationship between the mean GMV values of brain regions and the clinical features including psychological testing and mean retinal nerve fiber layer (RNFL) thickness in PACG groups were analyzed by using Pearson correlation. Compared with HCs, PACG patients showed significantly decreased GMV values in the left cerebellum posterior lobe (CPL), right extra-nuclear, and right superior temporal gyrus. In contrast, PACG patients showed significantly increased GMV values in the left CPL, right CPL, right superior temporal gyrus, right thalamus and right insula (P<0.01). Moreover, in the PACG group, the left mean RNFL showed a positive correlation with the mean GMV values of the left CPL (r=0.719; P<0.001) and the right mean RNFL showed a positive correlation with the mean GMV values of the left CPL (r=0.721; P<0.001). The Hamilton depression score showed a positive correlation with the mean GMV values of right insula (r=0.897; P<0.001). Our results demonstrated that PACG patients showed altered brain structure in various regions related to visuomotor function, thalamocortical pathway, and emotion function, which might provide a useful informations to understanding the anatomy neural mechanisms of deficit in vision loss and depression in PACG.