Evaluation of facial asymmetry generally involves landmark-based analyses that cannot intuitively assess differences in three-dimensional (3D) stereoscopic structures between deviation and non-deviation sides. This study tested a newly developed similarity index that uses a mirroring technique to intuitively evaluate 3D mandibular asymmetry, and characterised the resulting lower facial soft tissue asymmetry. The similarity index was used to evaluate asymmetry before and after surgery in 46 adult patients (27 men, 19 women; age, 22 ± 4.8 years) with skeletal Class III malocclusion and facial asymmetry who underwent conventional bimaxillary orthognathic surgery. Relative to the midsagittal plane used as the reference plane, the non-overlapping volume of the mandible significantly decreased, and the similarity index significantly increased after surgery. Similarity indexes of the mandible and lower facial soft tissue were strongly negatively correlated with non-overlapping volumes of each measurement. Differences in bilateral hemi-mandibular and hemi-lower facial soft tissue surface and volume measurements before surgery were significantly negatively correlated with similarity indexes of the mandible before and after surgery. This newly developed similarity index and non-overlapping volume using a mirroring technique can easily and intuitively evaluate overall 3D morphological discrepancies, especially 3D mandibular asymmetry, before and after surgery in skeletal Class III patients with facial asymmetry.