The efficacy of trans-sutural distraction osteogenesis therapy (TSDO) in treating midfacial hypoplasia in children with cleft lip and palate has been confirmed. However, few studies have reported that changes occur in the palate after TSDO treatment. To study the effect of TSDO on palatal morphology and its relative position in the craniofacial region, we retrospectively collected and measured the computed tomography images of 29 growing children with cleft lip and palate and midfacial hypoplasia, before and after TSDO. The results showed that the length and height of the palate did not change significantly, but the width and arch length increased, and the anterior area was more pronounced than the posterior area, with the median palatine suture still centered without obvious deviation. This suggests lateral palate growth after distraction, most likely around the median palatine suture. The distance from the palate to the cranial base also increased after distraction, and the anterior nasal spine moved forward, whereas the palate rotated by an average of 10.04° downward from the center of the anterior nasal spine. The increasing distance between the palate and cranial base may result from the growth of the nasal bone or the skull base. The oropharyngeal airway volume was also increased by an average of 2256.36 mm3, which may be beneficial to children's ventilatory function. In conclusion, TSDO therapy has influence on patients’ palatal morphology and position, which should be considered before surgery.