<p>Schizophrenia is a severe, highly disabling psychiatric disorder, and identification of early neurological indicators is essential for early diagnosis and targeted intervention. This study aimed to investigate brain structure in children with schizophrenia aged 9–10 years and to examine potential sex differences. We selected 10,332 eligible participants from the Adolescent Brain Cognitive Development (ABCD) study, of which 238 children with schizophrenia were screened by Kiddie Schedule for Affective Disorders and Schizophrenia (KSADS-5) diagnostic items, and propensity score was used to match the healthy group (<i>N</i> = 238). Nineteen regions of interest (ROI) closely related to schizophrenia, based on the previous reviews, were selected. Linear mixed-effects models were used to analyze the differences between children with schizophrenia and healthy children in the ROIs. Moreover, sex differences were further compared in brain regions significantly associated with schizophrenia. Our results indicated notable structural changes in several brain regions among children with schizophrenia compared to healthy controls. These regions included the left medial orbital sulcus, right central sulcus, right postcentral gyrus, right precentral gyrus, left lateral occipital temporal sulcus, and the right triangular part of the inferior frontal gyrus. Further comparisons on sex revealed that boys with schizophrenia had a significantly increased surface area of the right triangular part of the inferior frontal gyrus (Cohen’s d = -0.32) and reduced volume in the right postcentral gyrus (Cohen’s d = 0.31) and right central sulcus (Cohen’s d = 0.28) compared to girls. The findings suggest that sex-related structural differences may inform individualized neuromodulation and pharmacological strategies for schizophrenia.</p>