The education system of the Islamic Republic of Iran, as the main driver for realizing the New Islamic Civilization and the primary locus for nurturing the generation in line with the ideals of the Islamic Revolution, has consistently benefited from the wise guidance of the Martyred Leader of the Islamic Revolution. Aiming to explain the position of his thought in the educational policy-making system, the present study delineates an innovative model entitled The Geometry of Educational Policy-Making based on strategic charters, civilization-building statements, and the sublime thoughts of the Velayat-based governance. Within the theoretical framework of the geometry of policy-making in the Islamic educational system and focusing on three fundamental components—structural cohesion, value orientation, and operational efficiency—this paper seeks to analyze this invaluable managerial and strategic heritage. The main problem of this research is the allocative fragmentation resulting from the conflict of duties and parallel work within the four pillars of policy-making authorities, which is analyzed in this paper using a qualitative approach and thematic analysis of upstream documents and leadership guidelines. Within this framework, the Martyred Leader's statements are analyzed as orienting operators in a geometric structure, playing a decisive role in aligning policy-making bodies and integrating educational governance. The research findings indicate that this geometry, by establishing a triangular structure comprising structural cohesion, value orientation, and operational efficiency (based on the components of Educational Symmetry and Agile Governance), plays a fundamental role in shifting the paradigm from a purely education-oriented system to a civilization-building, upbringing-oriented one. This leadership model, while employing Intelligent Monitoring to map macro and sublime directions, strengthens inter-institutional cohesion and elevates the efficiency of the education system to the level of vast civilization-building capacities. Ultimately, the research demonstrates that the educational school of Velayat-based governance is a driving force that acts as an accelerator at all levels of the educational system within the policy-making layer, guaranteeing the movement of this institution toward the full realization of the authentic ideals of the Islamic Revolution and civilizational goals.