Objective There is growing evidence that reduced cortical thickness has been considered to be a central abnormality in schizophrenia. Brain imaging studies have demonstrated that the cerebral cortex becomes thinner in patients with first-episode schizophrenia. This study aimed to examine whether cortical thickness is altered in drug-naïve schizophrenia in a Chinese Han population and the relationship between cortical thickness and clinical symptoms. Methods We compared cortical thickness in 41 schizophrenia patients and 30 healthy controls. Psychopathology of patients with schizophrenia was assessed using the Positive and Negative Syndrome Scale (PANSS). Results The cortical thickness of left banks of superior temporal sulcus, left lateral occipital gyrus, left rostral middle frontal gyrus, right inferior parietal lobule and right lateral occipital gyrus in schizophrenia patients was generally thinner compared with healthy controls. Correlation analysis revealed a negative correlation between cortical thickness of the left banks of superior temporal sulcus and general psychopathology of PANSS. Conclusions Our results suggest that cortical thickness abnormalities are already present early in the onset of schizophrenia and are associated with psychopathological symptoms, suggesting that it plays an important role in the pathogenesis and symptomatology of schizophrenia. Key points (1) The first-episode drug-naïve schizophrenia had reduced cortical thickness than the controls. (2) Cortical thickness was associated with psychopathological symptoms in patients with schizophrenia.