Featuring a burning sensation in the tongue or other oral sites in the absence of observable lesions or laboratory findings, burning mouth syndrome (BMS) is a chronic intraoral pain disorder, which is one of the most common medically unexplained oral symptoms/syndromes. Previous studies have suggested that brain changes are involved in BMS; however, the small number of participants in these studies limited the conclusions that could be drawn. The present study aimed to further elucidate the brain anatomical and functional changes in BMS with a relatively large sample. Fifty-three patients (26 BMS patients and 27 gender- and age-matched controls) were recruited. Demographic information was collected interviews. Visual analogue scale (VAS), anxiety, and depression scale were administered. Participants underwent an MRI scan (including one high-resolution structural scan, one diffusion tensor image, and one session of resting state scan) on the same day. The results showed that BMS patients had higher depression and anxiety levels than controls. BMS patients showed lower gray matter volume (GMV) in the bilateral ventromedial prefrontal cortex (VMPFC) and increased functional connectivity between this region and the bilateral amygdala. Region of interest (ROI) analysis suggested that the functional connectivity between the bilateral VMPFC and amygdala correlated with the years of BMS illness in patients. The brain measures could predict the years of symptoms in the BMS group. These results suggest A potential neuromarker for the diagnosis and treatment of BMS.