The purpose of this study was to investigate the long-term effects of two-stage palatoplasty on the morphology of the maxillary alveolar arch and occlusion using plaster models of the maxilla and mandible obtained from patients with unilateral complete cleft lip and palate who also underwent orthodontic treatment. A total of 20 patients undergoing two-stage palatoplasty by Perko's method (Group T) were enrolled. Plaster models of the maxilla and mandible were obtained from each patient at Time 1, on commencement of orthodontic treatment in the mixed dentition period; at Time 2, on that of orthodontic treatment in the permanent dentition period; and at Time 3, on completion of active orthodontic treatment. Analysis of occlusion and morphological analysis were performed using a 3-dimensional measuring system. The results were compared with 15 patients who underwent one-stage palatoplasty by the push-back method using a mucoperiosteal flap (Group P). Alveolar morphology and the relationship between the maxilla and mandible were satisfactory in Group T. The palates in Group T were deeper and larger than those in Group P. Alveolar collapse in Group T was milder, and impairment of the alveolar morphology less notable than in Group P, as surgical invasion to the anterior alveolar region was avoided during the palatal growth period. These results suggest that two-stage palatoplasty is advantageous for jaw development.