Objective The aim of the study was to evaluate and support clinical application in periodontal disease of cone beam computed tomography(CBCT). Methods This study involved 4 patients with healthy periodontium who took the CBCT examination and compared with directly probing mesurement. Results The distance from gingival margin to alveolar crest, from gingival margin to cemento-enamal junction(GM-CEJ), from CEJ to alveolar crest mesured twice by the same observer which showed no statistical differences; the distance between gingival margin and alveolar crest, GMCEJ, CEJ and alveolar crest was mesured by two different observer which showed no statistical differences. The distances from GM-CEJ measured by CBCT were less than direct probing measurement, but the average difference was far more less than the minimum precision of the probe. Conclusion Periodontal measurement method by CBCT is practicable and repeatable and it is relatively precise to measure periodontal tissue by CBCT.