Objective To evaluate the teaching effect of case-based learning (CBL) combined with team-based learning (TBL) pedagogy in laboratory diagnostics education. Methods The data of the undergraduate clinical-medical students who completed the laboratory diagnostics course between September 2021 and July 2023 at West China School of Medicine of Sichuan University were retrospectively collected. Among them, the undergraduates of grade 2020 adopted the CBL+TBL combined pedagogy, while the undergraduates of grade 2019 assumed the traditional lecture-based learning (LBL) teaching method. Based on the cluster sampling method with the whole grade as the sampling unit, comparative effectiveness was assessed via examination scores and questionnaire feedback. Results A total of 303 students received the CBL+TBL teaching method (CBL+TBL group), while 289 students received the LBL teaching method (LBL group). Compared with the LBL group, the CBL+TBL group had higher scores on the clinical case discussion (90.28±4.05 vs. 88.39±5.19, P<0.001) while lower scores on the theoretical quiz (83.89±12.55 vs. 88.77±10.46, P<0.001). The overall performance of the CBL+TBL group was worse than the LBL group (61.28±3.83 vs. 61.98±3.98, P=0.028). A total of 161 valid copies of questionnaire were collected from the CBL+TBL group. Among them, more than 70% of the students believed that CBL+TBL pedagogy could improve learning motivation, independent learning ability, and team communication and assistance ability. Compared with the LBL teaching mode, 74.5% of the students preferred the CBL+TBL pedagogical approach. Conclusion The CBL+TBL pedagogy can help to improve autonomic learning, teamwork, and problem-solving ability, and a combination with LBL teaching may be utilized to enhance theoretical scores.