Objective To explore the effects of lecture-based learning (LBL), problem-based learning (PBL) or combination of both on the cardiovascular system anatomy teaching. Methods Nine classes majoring in clinical medicine of Grade 2009 were randomly divided into the LBL class, the PBL class and the PBL combined with LBL class. The examination scores and questionnaire were used to evaluate the teaching effect. Results The students of LBL class did well in the objective questions test, but badly in case analysis. On the contrary, the students of PBL class did well in case analysis, but were weak in objective questions test. However, the students of PBL combined with LBL class could get good grades in both of them. Questionnaire showed that the PBL teaching method, PBL and LBL combined method could improve their communicative ability, learning motivation, comprehensive analysis ability, language skills and so on. Conclusion Combination of PBL and LBL not only enhances students’ memories about the anatomic knowledge, but also helps students practice efficiently what they learned to analyze clinical cases. Furthermore, the method of PBL combined with LBL improves, to a certain extent, students’ comprehensive quality.