This paper explores the logic of scientific research management system of public hospitals in the new era,i-dentifying its connotations,principles,and pathways.From a value perspective,the system underscores the integration of effi-ciency and equity.In terms of governance logic,it advocates a shift from a single government-centric approach to a collaborative model that includes both government and market operation logics.The principles guiding transformation advocate for combination of ethical and market considerations,balance of rights and responsibilities,and integration of individual self-efficacy and organi-zational support.In terms of pathway selection,the paper proposes a comprehensive strategy that begins with forging a unified sci-entific research vision,serving as the foundation for creating a pedagogical organization to foster continuous learning,and the im-plementation of performance assessments based on core value.These strategies aim to modernize and enhance the efficiency of the scientific research management system in public hospitals.