Background: The cultivation of clinical reasoning and operative skills is the core of the practice course for undergraduates majoring in stomatology. To achieve this goal, a “discipline integration teaching method” is adopted in the practice course for root canal and prosthetic treatments in stomatology. Methods: A total of 893 students of West China School of Stomatology, Sichuan University, participated in this study. Of these students, 443 in the 2016-grade and 2017-grade groups used the traditional teaching method (Group TT) for preclinical practice courses (endodontics and prosthodontics training courses were taught separately), and 450 in the 2018-grade and 2019-grade groups used the discipline integration teaching method (Group DIT) for a preclinical practice course (root canal and prosthetic treatments were integrated into an endodontic‒restorative sequential treatment). The scores of the students (clinical skills examination and treatment planning) were compared between the two groups. In addition, students in Group DIT and their teachers were asked to complete a questionnaire on their attitudes and opinions about the DIT method in the preclinical course. Results: The results indicated that the DIT method was more effective than the TT method in enhancing students’ clinical reasoning and operational abilities. The questionnaire results showed that the teachers and students had recognized the DIT method. Conclusions: The DIT method significantly improved students’ learning quality and proved effective in the endodontic‒restorative sequential treatment practice course. This teaching method is expected to be further applied to other correlated subjects.