This study aimed to analyze the relationship between sex and corpus callosum (CC) volume in children with autism spectrum disorders (ASD) aged 2–4 years. This prospective study included 50 children with ASD and 50 typically developing (TD) children aged 2–4 years. Midsagittal slices of the CCs of the participants were divided into five subregions using FreeSurfer software. The PMCC, AMCC and TCC volumes were significantly higher in ASD participants than in TD participants, and results were significant in females with ASD rather than in males with ASD (all P < 0.05). In toddlers with ASD, the CC volumes were increased and more pronounced in females than in males. This could be due to overgrowth of axons or/and axonal pruning disorders.