Background/Objectives: Geometric morphometric analysis (GMA) is a statistical method that captures and quantifies shape variation. This study aimed to assess hard and soft tissue shape variations and changes following orthodontic treatment in Class III skeletal malocclusion using GMA. Methods: A retrospective study was conducted on 84 lateral cephalometric radiographs (pre-treatment and near-end treatment) of Class III patients aged 16–40 years (ANB < 2°). Thirty-five landmarks were digitized in Cartesian coordinates using MorphoJ software for shape analysis. Results: The sample included 62% females and 38% males, with a mean age of 24.7 ± 5.2 years. Vertical dimension variations (hypodivergent to hyperdivergent) contributed most to shape changes PC1 (23.35%), followed by anteroposterior variations PC2 (13.51%). Gender significantly influenced hard and soft tissue variation with 30.91%SS (F = 56.99, p < 0.0001). Males had significantly larger and longer ramus, body of the mandible, alveolar height, LAFH, TAFH and upper lip length. (PD: 0.026, p < 0.05). Significant shape changes were seen in the mandible (PD = 0.018, p < 0.05). SNB increased by 0.41° (from 81.73° ± 3.67°), and ANB improved by 0.46° but remained Class III (−0.33° ± 1.82°). Lower anterior facial height increased by 1.78 mm (p < 0.05). The lower incisors retroclined significantly (from 92° ± 8.56° to 87° ± 6.96°, p < 0.05), while the interincisal angle increased by 5.9°. Upper incisors remained procline (118° ± 11°, p > 0.05). Upper lip length increased by 0.4 mm (p < 0.05). Conclusions: Vertical and anteroposterior shape variations are notable within Class III malocclusion. Post-treatment changes in both hard and soft tissues indicate that orthodontic camouflage can enhance facial esthetics and skeletal balance. GMA provides objective quantification and visualization of these treatment-related craniofacial changes.