In the contemporary era defined by innovation-driven development and technology-led progress, scientific research capability has emerged as a pivotal component of professional competence for clinical medical practitioners. To align with the imperatives of modern medical education, clinicians must cultivate dual proficiency in clinical practice and scientific inquiry, thereby fostering the synergistic evolution of diagnostic-therapeutic excellence and research innovation. In recent years, the paradigm of bidirectional interaction, characterized by “research informing clinical practice and clinical challenges driving scientific discovery”, has gained substantial traction. High-quality scientific research not only drives advancements in clinical diagnostics and therapeutics, but also reinforces the professional identity of early-career physicians and amplifies the academic stature of medical institutions. However, within China’s current standardized residency training (SRT) system, a pronounced imbalance persists, wherein clinical skills are prioritized at the expense of research training. We systematically elucidate this disparity through a comparative analysis of Chinese and international SRT frameworks, critically examining the structural dilemmas confronting Chinese resident physicians. Drawing upon the research competency cultivation model implemented in Department of Gastroenterology at our institution, we propose a comprehensive strategic framework encompassing 4 dimensions: (1) developing an intelligent research infrastructure, (2) the optimization of mentor selection and development mechanisms, (3) the establishment of echelon-based research teams, and (4) the refinement of incentive and evaluation systems. These strategies aim to provide both theoretical underpinnings and practical guidelines for cultivating versatile, high-caliber medical professionals.