The 3D architecture of the mandible contributes to the functional and morphological characteristics of the lower one third of craniofacial region. The mandible has six distinct functional units, and its architecture is the sum of balanced growth of each functional unit and surrounding matrix. A dentofacial deformity (DFD) with malocclusion can be interpreted as their unbalanced growth. In order to characterize the mandibular 3D architecture, we analyzed the 3D reconstructed computed tomography (CT) images in terms of functional units. We evaluated both sides of 30 datasets of 3D CT scans of normal controls (N = 6) and patients with prognathic (N = 17) or retrognathic (N = 7) mandibles. We first identified and evaluated reference points to define mandibular functional units and compared their linear and angular measurements of DFD with normal group. The condylar and body length, the ratio of condyle/coronoid length, and the condylar head axis angle showed the statistically significant differences between groups. From these results, we could define the 3D reference points for functional units and identify the 3D architectural characteristics of DFD mandibles. These models may help us improve diagnosis and treatment planning to let them return to the normal and balanced architecture for DFD.