Objectives: The purpose of this study was to compare differences in facial soft tissue thickness in three-dimensional (3D) images before and after orthognathic surgery in patients with skeletal Class III malocclusion and to obtain a better understanding of the relationship between hard and soft tissue changes after surgery.Materials and method: The present retrospective study included 31 patients with skeletal Class III malocclusion with mandibular chin deviation greater than 4 mm who had undergone cone-beam computed tomography before and 6 months after surgery. Seven bilateral points were established. Measurements were taken from software-generated multiplanar reconstructions. The predictor variables were timing (pre- and postoperatively) and side (deviated vs.nondedicated). A regression model and correlation analysis were conducted for statistical analysis. Results: The difference of bilateral facial soft tissue thickness was statistically significantly different between deviated and nondeviated sides (P < 0.05), with lower values observed on the deviated side. The soft tissue thickness has become nearly symmetric at local regions of the lower thirds of the face after orthognathic surgery. However, most measurements showed a negative correlation between changes in soft tissue thickness and changes in bone tissues. Conclusions Skeletal Class III malocclusion with facial asymmetry is accompanied by differences in soft tissue thickness when comparing Dev and N-Dev sides of the posterior region of the mandible, where soft tissues are thinner on the Dev side. Soft tissue thickness can compensate for or camouflage the underlying asymmetric mandible. In addition, the asymmetric soft tissue thickness on the lower third of the face can be partially improved by orthognathic surgery, but the amount of soft tissue thickness change is not consistent with that of hard tissue positional change.