Abstract Objectives To compare the characteristics of mandibular asymmetry in patients with unilateral craniofacial microsomia (CFM) and class II asymmetry. Materials and methods Pretreatment cone-beam computed tomography of consecutive adults with Pruzansky-Kaban type I and IIA CFM (CFM group) was analyzed by 3D cephalometry. Fourteen mandibular landmarks and two dental landmarks were identified. The mandibular size and positional asymmetry were calculated by using landmark-based linear and volumetric measurements, in terms of asymmetry ratios (affected/non-affected side) and absolute differences (affected − non-affected side). Results were compared with non-syndromic class II with matched severity of chin deviation (Class II group). Statistical analyses included independent t test, paired t test, chi-square test, and ANOVA. Results CFM group (n, 21; mean age, 20.4 ± 2.5 years) showed significantly larger size asymmetry in regions of mandibular body, ramus, and condyle compared to Class II group (n, 21; mean age, 27.8 ± 5.9 years) (p < 0.05). The curvature of mandibular body was asymmetric in CFM. Regarding the positional asymmetry of mandibular body, while a comparable transverse shift and a negligible yaw rotation were found among the two groups, the roll rotation in CFM was significantly greater as well as the occlusal (6.06° vs. 4.17°) and mandibular (7.84° vs. 2.80°) plane cants (p < 0.05). Conclusions Mild CFM showed significantly more severe size asymmetry and roll rotation in mandible than non-CFM class II asymmetry. Clinical relevance To improve the mandibular size and positional asymmetry in CFM, adjunct hard tissue augmentation or reduction in addition to OGS orthodontics with a meticulous roll and yaw planning is compulsory, which is expected to be distinct from treating non-CFM class II asymmetry.