Objectives To assess the changes in alveolar bone of the mandibular second molars following molar protraction and investigate the factors associated with the alveolar bone changes. Materials and Methods Cone-beam computed tomography of 29 patients (mean age 22.0 ± 4.2 years) who had missing mandibular premolars or first molars and underwent molar protraction were reviewed. Alveolar bone level was measured as the distance from the cementoenamel junction at six points, buccal, lingual, mesiobuccal (MB), mesiolingual (ML), distobuccal (DB), and distolingual (DL), of the second molars at pretreatment (T0) and after molar protraction (T1). Factors associated with alveolar bone changes at the distal and mesial of the second molars were assessed. Results Mean alveolar bone changes ranged from −1.2 mm (bone apposition) to 0.8 mm (bone resorption). The presence of a third molar impaction at T0 (P < .001), third molar angulation at T0 (P < .001), and Nolla's stage of third molar at T0 (P = .005) were significantly associated with alveolar bone level changes distal to the second molars. Treatment duration (P = .028) was significantly associated with alveolar bone level changes mesial to the second molar. Conclusions Patients with impacted third molars, third molars at an earlier stage of development, and mesially angulated third molars at pretreatment may have less alveolar bone resorption distal to the second molars following protraction. Patients with increased treatment time may have reduced alveolar bone resorption mesial to the second molars.