Objective To explore the application effect of the 3D Slicer software-assisted case-based learning (CBL) teaching in the preoperative assessment teaching for epilepsy specialists. Methods Forty-six epilepsy specialist doctors who underwent advanced training in the neurology department's epilepsy ward of a hospital in Beijing from October 2022 to June 2023 were selected as the research subjects. They were randomly divided into the traditional teaching group and the 3D Slicer-assisted CBL teaching group. After completing the teaching sessions, the learning outcomes of both groups were assessed through theoretical examinations and the mini clinical evaluation (Mini-CEX) assessment scale. A questionnaire was also used to survey the learners' study interests and satisfaction. Results In the experimental group (3D Slicer-assisted CBL teaching group), the scores in the theoretical examination and Mini-CEX assessment were (84.04±3.56) and (23.87±1.14), respectively, both superior to those in the traditional teaching group of (77.57±4.25) and (21.57±1.38), with statistically significant differences (P<0.05). The experimental group members also exhibited higher levels of learning interest and satisfaction, compared to the control group. Conclusion The 3D Slicer-assisted CBL teaching model contributes to the mastery of cranial anatomy and preoperative epilepsy localization knowledge, enhancing teaching effectiveness. which is worth further exploration and promotion.