This study is aimed at investigating brain morphometry differences between children with ASD and healthy controls (HCs) in Saudi Arabia and exploring the association between IQ levels and brain volumes within the ASD group. Participants (N = 29, 31.1% females and 68.9% males) ranging in age from 6 to 17 years were scanned by MRI at the King Faisal Specialist Hospital and Research Center (KFSHRC). Brain volumes were analyzed while correcting for age, sex, and total intracranial volume (TICV). The analysis revealed that individuals with ASD exhibited larger volumes compared to HCs in the left caudate (p < 0.001), right caudate (p < 0.001), total caudate (p < 0.001), and total hippocampus (p = 0.014). These findings provide evidence for anatomical brain abnormalities in individuals with ASD and highlight the heterogeneity of these differences across brain regions. Furthermore, the analysis revealed that higher IQ levels were negatively associated with the volumes of the left thalamus, left pallidum, left accumbens area, right thalamus, right hippocampus, and total thalamus but positively correlated with the third lateral ventricle volume in HCs, p < 0.05. These results suggest a meaningful relationship between cognitive abilities, as measured by IQ, and variations in brain volumes in HCs. The study significantly contributes to the understanding of the neurobiology of ASD in a Middle Eastern population and emphasizes the importance of considering cognitive functioning in relation to brain morphology in ASD research and clinical practice.