The present study was aimed to investigate the relationship of the upper airway size and craniofacial structures in 3 dimensions in growing children of skeletal Class III. Forty-seven children (19 boys and 28 girls, 9.6 ± 1.3 years of age, range 8.0–12.4 years) were selected. Twenty-three children with normal vertical development were divided into groups of insufficient maxilla and overdeveloped mandible for the airway comparison between different sagittal skeletal patterns. Thirty-two children with the same sagittal development were divided into groups of low angle, normal angle, and high angle for the comparison between different vertical skeletal developments. The upper airway and craniofacial structures were measured in cone beam computed tomography images using DOLPHIN 11.7 software. Mann–Whitney U test and Kruskal–Wallis test were used to analyze the airway differences between groups. Spearman correlated analysis was done between the upper airway size and the craniofacial pattern in the transverse dimension. The results showed that the nasopharynx was the only affected airway part between groups of insufficient maxilla and overdeveloped mandible (P <0.05). The high angle group showed smaller upper airway compared with the groups of normal angle and low angle (P <0.05). The skeletal transverse dimension was correlated with the height of velopharynx, hypopharynx, and total airway with small gender differences.