Binocular depth inversion illusion (BDII), a visual, 'top-down'-driven information process, is impaired in schizophrenia and particularly in its early stages. BDII is a sensitive measure of impaired visual information processing and represents a valid diagnostic tool for schizophrenia and other psychotic disorders.However, neurobiological underpinnings of aberrant BDII in first-episode schizophrenia are largely unknown at present. In this study, 22 right-handed, first-episode, antipsychotic-naïve schizophrenia patients underwent BDII assessment and MRI scanning at 1.5T. The surface-based analysis via new version of Freesurfer (6.0) enabled calculation of cortical thickness and surface area. BDII total and faces scores were related to the two distinct cortical measurements. We found a significant correlation between BDII performance and cortical thickness in the inferior frontal gyrus and middle temporal gyrus (p < 0.003, Bonferroni corr.), as well as superior parietal gyrus, postcentral gyrus, supramarginal gyrus, and precentral gyrus (p < 0.05, CWP corr.), respectively. BDII performance was significantly correlated with surface area in the superior parietal gyrus and right postcentral gyrus (p < 0.003, Bonferroni corr.). BDII performance may be linked to cortical thickness and surface area variations in regions involved in "adaptive" or "top-down" modulation and stimulus processing, i.e., frontal and parietal lobes. Our results suggest that cortical features of distinct evolutionary and genetic origin differently contribute to BDII performance in first-episode, antipsychotic-naïve schizophrenia patients.