Physiology is an important basic course for medical majors. The content of the nervous system is abstract, the theories are profound, the knowledge is updated rapidly, and it is most closely connected with clinical practice. Students generally report difficulties in understanding, resulting in low learning interest. To improve teaching quality, this study has attempted to organically integrate clinical cases, scientific research methods and classroom teaching in the teaching of the nervous system, and constructed a “clinical-research-teaching” trinity teaching model. With “clinical problem-driven, scientific research thinking-driven, teaching scenario reconstruction” as the main line, real cases, scientific research examples and cutting-edge research progress in neuroscience were introduced to stimulate students’ learning interest and cultivate their scientific thinking and clinical application abilities. Practice has shown that this model can effectively improve teaching effectiveness and students’ comprehensive quality. Compared with the traditional teaching model, this teaching model significantly improved students’ final exam scores (p < 0.01), scores of the Critical Thinking Disposition Inventory (p < 0.01), and the number of approved college students’ innovation and entrepreneurship projects. It is proved that the “trinity” teaching model can stimulate learning interest, cultivate integrated medical talents, and is an effective way to achieve in-depth connection between basic medicine and clinical practice.