Abstract: The ideological security construction of university journals is a complex and dynamically evolving systematic project. The holistic national security perspective provides fundamental guidance and strategic direction for the ideological security construction of university journals, serving as a crucial platform for its implementation and reinforcement. Under the holistic national security perspective, challenges persist in the ideological security construction of university journals, including blind spots and deficiencies in risk identification and filtering mechanisms, threats to discourse dominance and the autonomy of knowledge production, and underutilized educational efficacy of implicit platforms. This study proposes that by employing political thinking, the ideological foundation can be strengthened, and the journal's foundational support solidified; through systematic thinking, discourse sovereignty can be contested, and the journal's core functions enhanced; and by applying scientific thinking, academic education mechanisms can be refined, and the strategic value of journals highlighted.