Objective To explore the effect of simulated cases and small group case discussion teaching in a modular course of clinical thinking training for medical students in the internship stage. Methods From June 2018 to January 2019, 40 clinical medical students enrolled in 2014 in Tongji University School of Medicine were randomly divided into experimental group (n=20) and control group (n=20). The experimental group was given DxR teaching module first, then group discussion module, and the control group was taught in the reverse order. Students' evaluation of teaching methods was got by questionnaire. Score of DxR clinician and tests by multiple choice questions were used to assess the teaching effect. Results 76.7% (31/40) students thought that DxR module was helpful to cultivate clinical thinking ability, and 90.0% (36/40) students liked group discussion teaching and thought it was helpful to cultivate clinical thinking ability. The scores of mid-term examination and DxR score in the later stage of control group were significantly higher than those in the experimental group [(75.4±13.5) vs. (66.7±10.7), 57.3 (53.7,59.0) vs. 46.0 (43.0,53.0), all P<0.01]; the overall performance of DxR in the latter stage of the control group was significantly higher than that in the former stage [57.3 (53.7,59.0) vs. 46.0 (39.0,48.7), P<0.01]. Conclusions This modular course conducted by DxR clinician and small group discussion was implemented smoothly and were highly accepted by students. Small group discussion module ahead of DxR module could improve the teaching effect of DxR probably by forming friendly learning atmosphere and enhancing learning initiative. The application of two teaching methods could complement each other and improve clinical thinking ability from different dimensions.