Limited accessibility, mountainous geography, and seismic conditions have posed challenges to both the preservation and the transmission of knowledge inherited from the Incas. Therefore, this research aims to analyze the ancestral Inca construction systems and their relationship with the Inca worldview through an architectural and structural study of the archaeological site of Choquequirao, located in Cusco, Peru. The research integrates geographic, climatic, spatial, functional, and constructive dimensions, applying digital 3D modeling tools (AutoCAD 2025, SketchUp 2024, and Sun-Path 2024) to assess the orientation, stability, and symbolic configuration of the main sectors. The results of the functional and constructive analysis reveal that Choquequirao incorporates adaptive principles in response to seismic and microclimatic conditions, as well as constructive typologies planned from an integral architectural perspective. These elements allow a clearer understanding of the spatial organization of the site and its cultural significance. Moreover, the study covers ten sectors distributed across 1800 hectares. The upper sector (4 ha) stands out for its architecture and political–ceremonial function; the lower sector (4 ha) includes ritual, administrative, residential, and storage areas for camelids; the southern sector (5 ha) contains the ushnu and priestly enclosures on terraces; and the eastern (7 ha) and western (2 ha) slopes integrate agricultural and residential uses. The study of Choquequirao highlights its complex organization and addresses contemporary challenges in terms of conservation and development. These findings provide essential insights for future restoration and conservation strategies that respect traditional construction systems and their environmental adaptation.