Accumulating evidence from brain structural imaging studies has supported that chronic pain could induce changes in brain gray matter volume. However, few studies have focused on the gray matter alterations of Trigeminal neuralgia (TN). In this study, twenty-eight TN patients (thirteen females; mean age, 45.86 years +/- 11.17) and 28 healthy controls (HC; thirteen females; mean age, 44.89 years +/- 7.67) were included. Using voxel-based morphometry (VBM), we detected abnormalities in gray matter volume in the TN patients. Based on a voxel-wise analysis, the TN group showed significantly decreased gray matter volume in the bilateral superior/middle temporal gyrus (STG/MTG), bilateral parahippocampus, left anterior cingulate cortex (ACC), caudate nucleus, right fusiform gyrus, and right cerebellum compared with the HC. In addition, we found that the gray matter volume in the bilateral STG/MTG was negatively correlated with the duration of TN. These results provide compelling evidence for gray matter abnormalities in TN and suggest that the duration of TN may be a critical factor associated with brain alterations.