The craniofacial morphology in patients with syndromic craniosynostosis varies from one spectrum to another. Our study aims to explore the craniofacial morphology and growth pattern in patients with Apert and Crouzon syndrome. This study involved 39 computed tomographic scans of skull (Apert = 11, Crouzon = 10, Control = 18), divided into 2 age subgroups. The non-parametric Mann-Whitney U test was performed to investigate the morphological characteristics between Apert, Crouzon and Control groups. The length of the middle cranial fossa decreased in both syndromes, but clivus length increased slightly in Apert syndrome and decreased in Crouzon syndrome. In Apert syndrome, midface height and width were control, and in Crouzon, the posterior height and width were slightly shorter, and the anterior side was control. The length of the midface was shortened in particular the upper segment. Zygomatic bone length and height as well as zygomatic arch length were developed close to control with a rotation in Apert syndrome. The zygomatic bones and arch in Crouzon syndrome were shortened in length and control in height without a rotation. The contributions of maxillary, zygomatic, and palatal deformities to midface malformation vary between two syndromes. Moreover, there was uneven severity of maxillary and zygomatic developmental deformities in both syndromes.