Objective: To develop a method for generating three-dimensional (3D) digital models of the periodontal ligament (PDL) using 3D cone-beam computed tomography (CBCT) reconstruction and to evaluate the accuracy and agreement of the 3D PDL models in the measurement of periodontal bone loss. Methods: CBCT data collected from four patients with skeletal Class III malocclusion prior to periodontal surgery were reconstructed at three voxel sizes (0.2 mm, 0.25 mm, and 0.3 mm), and 3D tooth and alveolar bone models were generated to obtain digital PDL models for the maxillary and mandibular anterior teeth. Linear measurements of the alveolar bone crest obtained during periodontal surgery were compared with the digital measurements for assessment of the accuracy of the digital models. The agreement and reliability of the digital PDL models were analyzed using intra- and interexaminer correlation coefficients and Bland–Altman plots. Results: Digital models of the maxillary and mandibular anterior teeth, PDL, and alveolar bone of the four patients were successfully established. Relative to the intraoperative measurements, linear measurements obtained from the 3D digital models were accurate, and there were no significant differences among different voxel sizes at different sites. High diagnostic coincidence rates were found for the maxillary anterior teeth. The digital models showed high intra- and interexaminer agreement. Conclusions Digital PDL models generated by 3D CBCT reconstruction can provide accurate and useful information regarding the alveolar crest morphology and facilitate reproducible measurements. This could assist clinicians in the evaluation of periodontal prognosis and establishment of an appropriate orthodontic treatment plan.