Background: Surgical correction of unilateral cleft lip and palate (UCLP) aims to restore normal facial development and function. Achieving symmetry is essential for dental arch development and facial symmetry. The surgical treatment can result in midfacial retrusion, maxillary constriction, and alveolar segment collapse. The aim of this study was to develop a novel 3D analysis method for assessing possible effects on maxillary arch development following different surgical techniques for lip repair in UCLP patients. Methods: The dimensions of the maxillary arch were analyzed and compared in children with UCLP who had undergone Delaire or Tennison-Randall/Pfeifer surgery before lip and palate closure using digitized dental plaster casts. Two different evaluation methods were used in the study: the 2D analysis was based on linear measurements using reference points in the OnyxCeph3™ software. The semi-automatic 3D analysis was based on the curve-fitting method and our self-developed customized software application (SMP). Results: No significant differences were observed using the 2D method. However, the 3D analysis detected statistically significant differences in the Q coefficient (p = 0.001393) between the two surgical techniques, demonstrating the superior ability of the 3D method to assess morphological changes. Conclusions: The 3D analysis did not depend on classical reference points. It provided new information for assessing the collapse of maxillary segments. This analysis is a valuable tool for evaluating the impact of surgical techniques on maxillary arch development in children with UCLP. These findings advocate the integration of advanced 3D imaging tools in cleft surgery planning and postoperative assessment.