Anorexia nervosa (AN) is a mental disorder characterized by a preoccupation with thinness and may be associated with brain structural alteration. The aim of the study was to examine the brain structural alteration in AN patients, including subcortical structure volume and cortical thickness. Thirty-five un-medicated AN patients and 20 matched healthy controls underwent structural magnetic resonance imaging brain scans. High resolution structural images were acquired on a SIEMENS 3T scanner and preprocessed using FreeSurfer software. Subcortical structure volume and cortical thickness were compared between the two groups. We found larger percentage of caudate volume relative to total grey matter (GM) volume in the AN group. Reduced cortical thickness at the left precuneus was also observed in AN patients. Moreover, an interaction between group and hemisphere was found, suggesting that cortical thinning was more prominent in the left hemisphere in AN patients. These findings provide further evidence for structural brain abnormalities in patients with AN.