The importance of early diagnosis of pediatric malocclusion and early intervention has been emphasized. Without use of radiation, 3D imaging holds the potential to be an alternative for evaluating facial features in school-aged populations. Students aged 9 and 10 years were recruited. We performed annual 3D stereophotogrammetry of the participants' heads. A total of 37 recognizable anatomical landmarks were identified for linear, angular, and asymmetric analyses using the MATLAB program. This study included 139 healthy Taiwanese children with a mean age of 9.13, of whom 74 had class I occlusion, 50 had class II malocclusion, and 15 had class III malocclusion. The class III group had lower soft-tissue convexity (p = 0.01) than the class II group. The boys with class II malocclusion had greater dimensions in the anteroposterior position of the mid-face (p = 0.024) at age 10. Overall asymmetry showed no significance (p > 0.05). Heat maps of the 3D models exhibited asymmetry in the mid-face of the class II group and in the lower face of the class III group. Various types of malocclusion exhibited distinct facial traits in preadolescents. Those with class II malocclusion had a protruded maxilla and convex facial profile, whereas those with class III malocclusion had a less convex facial profile. Asymmetry was noted in facial areas with relatively prominent soft-tissue features among different malocclusion types.