This study aims to elucidate the spatial coherence of traditional Iranian schools through the integration of two-dimensional space syntax analysis with the evaluation of sectional and three-dimensional spatial components. The research adopts an analytical-comparative approach, examining eight historical schools through Visibility Graph Analysis (VGA). In the first stage, the spatial syntax indicators, including visual connectivity, visual integration, control, mean depth, and intelligibility, were extracted using Depthmap software. In the second stage, physical -sectional and morphological- components, including courtyard enclosure ratio, vertical hierarchy, façade permeability, number of floors, spatial covering systems, and vertical visual axes, were measured or estimated based on plans, sections, elevations, and physical information of the selected cases. Subsequently, the results of the two analytical levels were compared and interpreted through an integrated matrix. The findings indicate that the central courtyard is the primary organizing element of visual and movement relationships in all examined cases, while two-dimensional analysis alone is insufficient to fully explain spatial experience. Among the studied samples, Khan School in Shiraz demonstrated the highest configurational coherence, with a mean visual integration value of 16.82 and an intelligibility coefficient of 0.97. The sectional and three-dimensional analysis further revealed that courtyard centrality is not solely dependent on horizontal plan relationships but is also associated with the height-to-width ratio of the courtyard, the hierarchy between chambers, arcades, iwans, and teaching spaces, the degree of façade openness, and the structural characteristics of major covered spaces. Khan School, with an approximate vertical hierarchy index of 1.82 and greater façade openness, showed the strongest convergence between horizontal plan centrality and the vertical emphasis created by its iwans. Conversely, in Aqa Bozorg School in Kashan, the approximate vertical hierarchy index of 2.43, together with the domed chamber, elevated iwan, and differences in courtyard levels, contributed to compensating for certain limitations in plan-based intelligibility. The results demonstrate that integrating space syntax analysis with the assessment of height, enclosure, openness, level differences, and roof structures provides a more comprehensive framework for understanding the spatial organization of traditional Iranian schools.