Purpose Cephalometric evaluation of craniofacial and craniopharyngeal morphology is important for understanding the factors affecting velopharyngeal dysfunction (VPD) in patients with palatal anomalies. Materials and methods In this study, 366 patients with VPD were retrospectively stratified into cleft lip and palate (CLP), cleft palate (CP), submucous cleft palate (SMCP), occult submucous cleft palate (OSMCP), and non-CP groups. Lateral cephalometrics were used to assess craniofacial, craniopharyngeal, and velopharyngeal anatomy. Results The average craniofacial morphology in patients with VPD differed significantly according to the type of palatal anomaly. The non-CP and OSMCP groups differed from the CLP, CP, and SMCP groups in nasopharyngeal size and shape as depicted by a larger ANS–Ptm–Ve angle, a smaller S–N–Ba and NBa–PP angles, and a shorter linear value of S–Ar in the non-CP group. The CLP and CP groups had shorter ANS–Ptm, shorter Ptm–P, and smaller SNA and SNB angles. Conclusion VPD patients with overt clefts have different skeletal and nasopharyngeal shapes compared to non-CP and OSMCP. Velopharyngeal function assessment should include the size and shape of the nasopharyngeal space in addition to the size and the activity of the velum and posterior and lateral walls of the nasopharynx. This should enable a more precise understanding of VPD pathology, and lead to improvements in the posterior pharyngeal flap technique in order to obtain better postoperative speech outcomes after surgical management of velopharyngeal dysfunction.