Objective To explore the application of a case database of 3D virtual simulation patients with typical periodontal diseases in pre-clinical periodontal education. Methods Thirty stomatological students from Peking University, enrolled in 2018, who were about to enter the clinical practice of periodontology, were recruited as the research objects. And the students were randomly divided into the control group and the study group, 15 in each group. The study group received training using the case database of 3D virtual simulation patients with typical periodontal diseases, while the control group received traditional teaching. After the training, the two groups were assessed on their clinical skills using the case database, and were scored by the system. The students were asked to fill in the feedback questionnaire to evaluate the case database. The t-test was used to compare the differences between the two groups. Results The mean score of history collection of the study group [(52.67±16.24) points] was higher than the control group [(36.80±10.84) points], and the difference was statistically significant (t=3.15, P=0.004). The results of the questionnaire show that all students fully agree or agree that this case library can enhance the ability and confidence of periodontal clinical reception. Conclusions The case database of 3D virtual simulation patients with typical periodontal diseases can improve the periodontal clinical consultation ability of stomatological students, and its efficacy was also widely recognized by students. The case database is expected to be further popularized and applied in the pre-clinical education.