Malocclusions result from the interaction between craniofacial growth, mandibular morphology, and neuromuscular function. The dimensions and shape of the mandibular body and ramus, mandibular plane inclination, condylar position and morphology, skeletal symmetry, and bone quality are associated with different patterns of masseter and temporalis muscle activity and with different modes of mandibular movement control. Hyperdivergent subjects often show lower biomechanical efficiency and reduced muscle strength, whereas hypodivergent patterns are generally characterized by stronger muscles and higher occlusal loads. These features may influence both the response to functional orthodontic treatment and orthodontic–surgical planning. In growing patients, the effectiveness of functional appliances depends not only on residual growth potential, but also on mandibular growth direction, joint geometry, and the capacity for muscular adaptation. In surgical patients, muscle vector orientation, ramus height, skeletal asymmetries, and vertical dimension control may affect the magnitude of surgical movements, postoperative stability, and the risk of relapse. Following treatment, the mandible, temporomandibular joint, and masticatory muscles undergo remodeling and adaptation. Electromyographic activity and bite force may temporarily decrease after surgery and progressively recover, whereas functional treatment may modify muscle recruitment and motor control. However, achieving a satisfactory occlusion does not necessarily imply normalization of function.