Driven by the construction of "New Medical Sciences" and the educational digitalization strategy, there is an increasingly urgent demand in medical education for compound talents who possess a solid professional foundation, scientific research literacy, and clinical innovation capabilities. To address the problems existing in traditional physiology courses—including insufficient training of high-order thinking, delayed scientific research initiation, and a single evaluation mechanism—this study, with the concept of outcome-based education (OBE) as the guide and supported by constructivist and inquiry-based learning theories, has constructed and implemented a new "Teaching-Learning-Research Integration" blended online-offline curriculum model for physiology. The curriculum promotes reforms systematically from four dimensions. First, in the online dimension, it upgrades resources such as micro-courses and virtual simulation experiments, and optimizes self-directed learning paths. Second, in the offline dimension, it reconstructs flipped classrooms to strengthen the discussion of scientific research cases and interactive inquiry. Third, it expands in-depth scientific research guidance and builds a stepped scientific research training system through SRIP projects and discipline competitions. Fourth, it reforms the multi-dimensional evaluation mechanism by integrating process-oriented assessment and scientific research literacy evaluation. The practical results show that students’ mastery of basic physiology knowledge has been significantly improved; the effectiveness of cultivating their scientific research literacy and professional literacy, as well as their overall course satisfaction, have all been enhanced. Meanwhile, the teaching and research capabilities of the teacher team have been synchronously strengthened, achieving the goal of “mutual promotion between teaching and research”. This study confirms the effectiveness and promotion value of the in-depth integration of “Teaching-Learning-Research” in physiology courses. It provides a replicable and transferable model reference for the reform of basic medical courses under the background of “New Medical Sciences” and holds important practical significance for systematically improving the scientific research literacy and innovation capabilities of medical talents.