Model analysis was performed to identify palatal rugae anatomical morphology patterns, evaluate their individual-specific properties and stability before and after orthodontic treatments, and investigate their reliability in the use for individual identification from the perspective of forensic dentistry. Maxillary models of 70 patients were collected before and after orthodontic treatments, palatine images were taken under standard conditions. Pattern-based individual identification was performed through measuring some indices including changes in number, orientation, shape, and length of palatal rugae, as well as mesial and distal endpoint displacement of palatal rugae in the anteroposterior (AP) and mesiodistal (MD) direction. At the same time, maxillary models of 10 patients were randomly selected for individuality confirmation and the average rate of correct matches was calculated. palatal rugae anatomical morphology patterns were highly individual-specific. Palatine of the same pattern were not found before or after orthodontic treatment. Model-based analysis confirmed the high individual-specificity properties of the palatal rugae anatomical morphology patterns, and also showed that the incidence of any morphological change in the patterns after orthodontic treatment was 45.7 % for anteroposterior displacement of the distal endpoint of palatal rugae, 40 % for mesiodistal displacement of the distal endpoint of palatine, 32.9 % for anteroposterior displacement of the mesial endpoint of palatal rugae, and 17.1 % for mesiodistal displacement of the mesial endpoint of palatal rugae. The incidence of change in length, orientation and shape of palatine after orthodontic treatment was 28.6 %, 1.4 % and 1.4 % respectively; and the incidence of palatal segmentation and unification after orthodontic treatment was 4.3 % and 2.9 % respectively. The mean percentage of correct matches of the palatine patterns after orthodontic treatment to their duplicates was 99.05 % and the mean percentage of correct matches of the palatine patterns between before and after orthodontic treatment was 92.19 %. Palatal rugae anatomical morphology patterns are unique to each individual. After orthodontic treatment, palatal rugae have diverse presentation patterns. Although the diverse palatine patterns to a certain degree, influence individual identification in the field of forensic identification, palatal rugae patterns can be used as a novel method for individual identification in forensic dentistry.