Although previous studies have demonstrated an association between metabolic syndrome (MS) and changes in the integrity of cerebral white matter, no study has evaluated cortical thickness or subcortical volumes in MS with MRI. The purpose of our study was to investigate changes in cortical thickness and subcortical volume in an asymptomatic MS population. A total of 86 asymptomatic subjects (40 patients with MS and 46 subjects without MS) underwent 3T brain MRI scanning, and cortical thickness was compared between the groups across multiple locations. The subcortical volumes were also compared on a structure-by-structure basis. ANCOVA adjusted for age, education, total intracranial volume (TIV), and gender revealed significant volume reductions in the right nucleus accumbens in the MS group compared with the control group. The MS group showed a significant reduction in mean cortical thickness and volume in both hemispheres compared with controls. A group comparison analysis of the regional cortical thickness between the two groups also revealed significant reductions in cortical thickness in the MS group in the left insular, superior parietal, postcentral, entorhinal, and right superior parietal cortices compared with those of the control group (all comparisons p < 0.05, FDR corrected). We demonstrated a significant reduction in cortical and subcortical areas in MS patients, especially in areas involved in body weight control and cognitive function. Our results suggest an initial neurodegenerative process according to metabolic syndrome even in the preclinical stage, and further prospective studies are required to evaluate this process.