This study examined the morphology of frontal-parietal regions relevant to motor functions in children with autism spectrum disorder (ASD) with or without attention deficit hyperactivity disorder (ADHD). We also explored its associations with autism severity and motor skills, and the impact of comorbid ADHD on these associations. Participants included 126 school-age children: 30 had ASD only, 33 had ASD with ADHD, and 63 were typically developing. High resolution 3T MPRAGE images were acquired to examine the cortical morphology (gray matter volume, GMV, surface area, SA, and cortical thickness, CT) in three regions of interest (ROI): precentral gyrus (M1), postcentral gyrus (S1), and inferior parietal cortex (IPC). Children with ASD showed abnormal increases in GMV and SA in all three ROIs: (a) increased GMV in S1 bilaterally and in right M1 was specific to children with ASD without ADHD; (b) all children with ASD (with or without ADHD) showed increases in the left IPC SA. Furthermore, on measures of motor function, impaired praxis was associated with increased GMV in right S1 in the ASD group with ADHD. Children with ASD with ADHD showed a positive relationship between bilateral S1 GMV and manual dexterity, whereas children with ASD without ADHD showed a negative relationship. Our findings suggest that (a) ASD is associated with abnormal morphology of cortical circuits crucial to motor control and learning; (b) anomalous overgrowth of these regions, particularly S1, may contribute to impaired motor skill development, and (c) functional and morphological differences are apparent between children with ASD with or without ADHD.