Objective To evaluate the effect of two -phase treatment on upper airway dimensions in skeletal Class Ⅲ malocclusions. Methods 18 patients with skeletal Class III malocclusion with crowding in dentition were included. These patients were consecutively treated with two phase. Lateral cephalometric radiographs were used to quantify the skeletal and upper airway changes before treatment(T1), after maxillary protraction(T2) and after treatment(T3), and t test was assessed to compare the significant difference between the three groups. Results The dimensions of S-PNS, Ad1, Ad2, AA-PNS, SPS increased significantly(P<0.05), IPS decreased significantly (P<0.05). The change of eb-Peb was not significant(P>0.05). Conclusions In young individuals with skeletal Class Ⅲ malocclusion with crowding diagnosed with maxillary deficiency treated with two-phase treatment, the upper airway dimensions were affected after the treatment, and favorable effects of the treatment appeared in nasopharynx airway.