Ability of clinical decision-making is one of the essential capacities of doctors, as well as one of the necessary and important training objectives in medical education. At present, there is no complete system for training this ability of medical students. Usually, it is too late to arrange the training program in the senior stage. It is worth exploring and researching how to integrate the cultivation of clinical decision-making ability into the basic courses in lower grades, in order to training as soon as possible. This study took the course of medical genetics as an example, combined the characteristics of inquiry teaching method, simulated various sub-modules of clinical decision-making thinking process, optimized course design, and explored the integration of clinical decision-making ability cultivation in lower grade courses. The results suggest that inquiry teaching design can fully mobilize students’ initiative and increase their investment diving in analysis and thinking. Under the guidance of teachers, it can effectively promote students’ training in the process of clinical decision-making thinking process. Finally, the ideas for thinking strand design and practice were analyzed, the design principles and key points were summarized, and the gains and losses in teaching were reflected as well.