Abstract Cone-beam computed tomography (CBCT) enhances understanding of the upper airway (UA). This study compared three software products’ abilities in visualizing and quantifying specific upper airway changes using CBCT. We conducted a retrospective analysis of pre- and post-operative CBCT images from 29 patients using Dolphin (Do), Romexis 5 (Ro5), and Romexis 6 (Ro6) software, focusing on alterations in oropharyngeal volume and minimum cross-sectional area as key indicators of orthognathic surgery outcomes. ANOVA analysis showed significant differences in volume measurements between Do/Ro5 ( p = 0.034) and Do/Ro6 ( p = 0.047), but no difference between Ro5 and Ro6 ( p = 0.685). No significant differences were found in minimum cross-sectional area parameters. Despite standardized protocols, interpretation discrepancies exist between Do and Ro 5/6, possibly due to program-specific properties. Further studies on threshold value comparability are needed for data standardization. Direct comparisons of clinical data from Do, Ro5, and Ro6 are limited due to methodological disparities. Nonetheless, these programs allow reproducible and quantifiable measurements for clinical assessments of these specific airway changes following orthognathic surgery.