This paper explores the role and risk management strategies for scientific technological, and medical (STM) journals within the framework of the Overall National Security Concept (ONSC) in China. Through a comprehensive policy-theoretical framework grounded in the ONSC, this study employs multiple research methods, including theoretical analysis, case studies, and inductive-deductive reasoning to systematically investigate how STM journals contribute to and interact with the broader landscape of national security. This study highlights the multifaceted functions of STM journals in enhancing national technological security, strengthening national soft power, safeguarding economic security, and consolidating strategic security. Additionally, it identifies a series of security risks inherent to STM journals that could potentially undermine overall national security. This study establishes the conceptual linkage between STM journals and overall national security by referencing National Security Law and other related regulations. It further examines five major categories of security risks associated with STM journals under the ONSC perspective. First, the risk of sensitive technology leakage is addressed, emphasizing that while STM journals facilitate open academic exchange, they simultaneously pose threats of critical information exposure that may affect military and economic security. Multiple documented cases of inadvertent disclosure of sensitive technologies highlight the urgency of stringent review protocols. Second, ideological security risks arising from political errors in publication content are analyzed, stressing the necessity of rigorous political review to avoid misinformation that could damage national cohesion and international relations. Third, the study discusses the impact of academic fraud on innovation security, noting increasing incidents of scientific misconduct that undermine trust and waste resources, thereby threatening the integrity of national scientific advancement. Fourth, ethical risks related to incomplete or flawed academic review procedures are considered. Fifth, social public opinion risks triggered by inappropriate content publication are identified, which may escalate into broader social disputes through rapid dissemination on digital platforms. To address these intertwined risks, this paper proposes a comprehensive risk management framework tailored to the realities of STM journals under the ONSC. Recommendations include: First, establishing dedicated review committees for sensitive technology to prevent information leakage; Second, implementing stringent political review processes to safeguard ideological security; Third, enhancing academic integrity mechanisms by combining technological tools and expert peer review to identify and prevent misconduct; Fourth, improving academic review systems to ensure ethical compliance and scientific rigor; Fifth, developing emergency response mechanisms to effectively manage social opinion crises. In conclusion, this study provides a theoretical and practical foundation for further scholarly inquiry and policy development to enhance the security governance of STM journals in the context of China’s overall national security strategy.