This study aimed to evaluate the effect of orthognathic surgery on masseter volume in patients with skeletal Class III malocclusion with facial asymmetry and the effect of masseter volume on stability in orthognathic surgery. This research studied 16 patients with Class III malocclusion with facial asymmetry who received combined orthodontic-orthognathic treatment and underwent craniofacial computed tomography (CT) before (T0), 2 weeks after (T1), and 6 months after (T2) surgery. Three-dimensional (3D) CT images were retrospectively analyzed, using 3D volume reconstruction to obtain the masseter volume and examine the impact of the masseter volume on stability in orthognathic surgery. A statistically significant difference ( P < 0.05) in the volume of the masseter was found up to 6 months after orthognathic surgery compared with the preoperative period, and the reduction in the masticatory muscle volume on the lengthened side is greater than on the shortened side ( P < 0.05). The volume of both masseters differed according to facial asymmetry, and the difference was significantly reduced after orthognathic surgery ( P < 0.05). During the period time (T1-T2), cephalometric maxillary marker points were not significantly different ( P > 0.05), and mandibular marker points were significantly anteriorly shifted ( P < 0.05). There was an association between the masseter volume and anterior shift of point B (R > 0.5, P < 0.05), the upward and anterior shifts of the gonion point differed between the lengthened and shortened sides ( P < 0.05). The size of the masseter becomes smaller 6 months after orthognathic surgery, and orthognathic surgery improves both bone and soft tissue symmetry. A larger sagittal relapse of mandibular setback occurred in patients with greater masseter volume. Considering these alterations may be helpful in planning orthognathic surgery.