Objectives: Quantitative assessment of 3-dimensional progressive changes of the maxillary geometry in unilateral cleft lip palate (UCLP) with and without nasoalveolar molding (NAM). Methods: The study was designed as a prospective 2-arm randomized controlled clinical trial conducted in parallel. Forty infants with nonsyndromic UCLP were randomly assigned into a NAM-treated group (n = 20) and non–NAM treated group (n = 20). A total of 120 laser-scanned maxillary casts were collected and blindly analyzed via a modified algorithm at T0 (initial visit; baseline), T1 (after 3 wk; first interval), and T2 (after 6 wk; second interval). The main outcome measures were the amount and rate of cleft gap changes, the midline position, and the transverse, sagittal, and vertical growth through intervals. Results: More than 50% of the cleft gap (56.42%; P < 0.001) was reduced in the first 3 wk of alveolar molding (AM). The end point of the AM was obtained in 6 wk (86.25%; P < 0.001); then, the kinks of the greater segment were noticed. The AM effect decreased as far as posterior; the anterior arch width reduced slightly (1.23%; P < 0.001), while the middle and posterior arches increased slightly (P > 0.999 and P = 0.288, respectively). The posterior arch width was the least changing and was considered a baseline, while the anterior was the pivot of the segment rotation. Both groups showed different patterns of segment rotation and sagittal growth. The non–NAM treated group showed a slight increase in cleft gap length, arch width, and midline position. Conclusion: Based on this study, it was concluded that the NAM treatment is effective in minimizing cleft severity and realigning maxillary segments without the deterioration of the transverse and vertical arch growth. Near follow-up visits are recommended to monitor the rapid gap reduction within the first 3 wk. Further trials are recommended to compare the outcomes regarding the sagittal growth to reference values ( ClinicalTrials.gov NCT03029195). Knowledge Transfer Statement: The results of this study will help clinicians understand nasoalveolar molding biomechanics that may improve the treatment outcomes for patients with unilateral cleft lip and palate. The trial data can be a valuable guide to the qualitative and quantitative predictive virtual molding in computer aided design–simulated nasoalveolar molding therapy. The modified algorithm can be used by researchers to quantify the rate, the sequence, and the direction of the maxillary segments movement in unilateral cleft lip and palate.