Iranian architecture during the Safavid period underwent significant transformations in spatial organization, geometry, hierarchy, and aesthetic qualities, coinciding with the emergence of a new political-religious structure and the expansion of intellectual and philosophical currents. Among these, Transcendent Philosophy (al-Hikmah al-Muta‘aliyah), developed by Mulla Sadra, emphasized concepts such as existence, the gradation of being (tashkik al-wujud), unity and multiplicity, substantial motion, and the hierarchical order of existence. These concepts provide a theoretical framework for examining the relationship between philosophical thought and architectural space. This study aims to explain the relationship between Transcendent Philosophy and the spatial organization of Iranian architecture from the Safavid to the Qajar periods by examining the reflection, continuity, transformation, and reinterpretation of related principles. Adopting a qualitative approach, the research employs historical, discourse, and comparative analysis within a conceptual framework connecting “thought, society, and space.” The findings indicate that the relationship between Transcendent Philosophy and architecture cannot be reduced to a direct translation of philosophical concepts into architectural forms. Rather, it emerged through the interaction of intellectual systems, socio-historical conditions, architectural traditions, and societal needs. In Safavid architecture, principles such as centrality, spatial hierarchy, geometric order, proportion, integration of part and whole, and spatial sequence can be interpreted through certain concepts of Transcendent Philosophy. Architectural transformations from the Safavid to the Qajar period demonstrate “dynamic continuity,” whereby these principles were reinterpreted in response to changing political, social, urban, and cultural contexts. Thus, continuity appears primarily through the persistence and reinterpretation of semantic, spatial, and aesthetic logics.