Objective: To establish a similarity measurement model for patients with dentofacial deformity based on 3D craniofacial features and to validate the similarity results with quantifying subjective expert scoring. Methods: In the study, 52 cases of patients with skeletal Class Ⅲ malocclusions who underwent bimaxillary surgery and preoperative orthodontic treatment at Peking University School and Hospital of Stomatology from January 2020 to December 2022, including 26 males and 26 females, were selected and divided into 2 groups by sex. One patient in each group was randomly selected as a reference sample, and the others were set as test samples. Three senior surgeons rated the similarity scores between the test samples and the reference sample. Similarity scores ranged from 1 to 10, where 1 was completely different, and 10 was exactly the same. Scores larger than 7.5 was considered as clinically similar. Preoperative cone beam computed tomography (CBCT) and 3D facial images of the patients were collected. The three-dimensional hard and soft tissue features, including distances, angles and 3D point cloud features were extracted. The similarity measurement model was then established to fit with the experts' similarity scoring by feature selection algorithm and linear regression model. To verify the reliability of the model, 14 new patients were selected and input to similarity measurement model for finding similar cases. The similarity scoring of these similar cases were rated by experts, and used to evaluate the reliability of the model. Results: The similarity metric models indicated that the features of the middle and lower craniofacial features were the main features to influence the craniofacial similarity. The main features that were related to the expert' s similarity scoring included distance of anterior nasal spine-menton (ANS-Me), distance of right upper canion point-Frankfurt horizontal plane (U3RH), distance of left superior point of the condyle-left gonion (CoL-GoL), distance of left gonion-menton (CoL-Me), distance of pogonion-midsagittal plane (Pog-MSP), distance of right alar base-left alar base (AlR-AlL), angle of pronasale-soft tissue pogonion-labrale inferius (Pn-Pog' -Li), distance of trichion-right tragus (Tri-TraR), distance of left exocanthion-left alar base (ExL-AlL), lower 1/3 of skeletal face, middle and lower 2/3 of skeletal face and upper lip region of soft tissue. Fourteen new patients were chosen to evaluate the model. The similar cases selected by the model had an average experts' similarity scoring of 7.627± 0.711, which was not significantly different with 7.5. Conclusion: The similarity measurement model established by this model could find the similar cases which highly matched experts' subjective similarity scoring. The study could be further used for similar cases retrieval in skeletal Ⅲ malocclusion patients.