Objective: To explore the effect of PBL teaching method combined with mini CEX in the teaching of organ system integration course. Methods: 20 students of 2019 grade organ system integration motor system were selected as the experimental group, and 20 students in the same class were selected as the control group., PBL combined with mini CEX method and traditional teaching method are used for teaching respectively. After learning, theoretical evaluation and mini CEX form are carried out to compare the evaluation results and evaluate the teaching effect. Results: the scores of theoretical evaluation and mini CEX of students in the experimental group were better than those in the control group (P < 0.05). Conclusion: PBL combined with mini CEX is effective in the teaching of organ system integration course, which can improve students' clinical ability and is worthy of further promotion.