A system-oriented curriculum in which basic medical courses and clinical subjects are integrated and reformed is a new trend for medical education in China. In order to train and enhance the comprehensive clinical competency, thirty-two excellent medical students who formed a observation group from grade 2010 in Jinan University were selected to participated in this study. Three different exploratory and heuristic pedagogies, which employed the flexible application of case-based learning (CBL), problem-based learning (PBL), and team-based learning (TBL), were explored and implemented in cardiovascular, respiratory, and digestive teaching sections. The effects of these exploratory and heuristic pedagogical approaches based on the flexible application of the CBL, PBL, and TBL methods with clinical scenarios in system-oriented curricula are satisfactory. Accordingly, these teaching methods and experiences had been summarized and promoted to mainland and non-mainland medical students from grade 2014 in Jinan University. Teaching and learning effects are also satisfactory. In addition, different characteristics in conducting these courses between two types of university students are further compared and analyzed for the improvement of all system-oriented curricula in the future.