Functional constipation (FC) is a common functional gastrointestinal disorder (FGID). Neuroimaging studies on patients with FC showed brain functional abnormalities in regions involved in emotional process modulation, somatic and sensory processing and motor control. Brain structural imaging studies in patients with FGID have also shown disease-related alterations in cortical morphometry, but whether and how FC affects brain structure remains unclear. Structural Magnetic Resonance Imaging and surface-based morphometry analysis were used to investigate the impact of FC on cortical morphometry in 29 patients with FC and 29 healthy controls (HC). Results showed that patients with FC compared to HC had significantly decreased cortical thickness in the left middle frontal gyrus (MFG), dorsomedial (DMPFC) and ventromedial prefrontal gyrus (VMPFC), right dorsal anterior cingulate cortex (dACC), left orbitofrontal cortex (OFC), posterior cingulate cortex (PCC)/precuneus, middle temporal gyrus (MTG), and supplementary motor area (SMA) (P < 0.01). Correlation analysis showed that sensation of incomplete evacuation was negatively correlated with cortical thickness in the SMA (P < 0.0001). In addition, patients with FC also had decreased cortical volume than HC in the MTG, precentral gyrus (PreCen) and precuneus/cuneus (P < 0.01), as well as decreased cortical surface area in the PreCen (P < 0.01). No correlation was found between cortical volume/surface area and behavioral measures. These findings suggest that patients with FC are associated with cortical morphometric abnormalities in brain regions implicated in somatic/motor-control, emotional processing and self-referential processing.