As a UNESCO World Heritage Site, the Great Wall's site selection strategy embodies a nuanced interplay of geographical environmental intelligence, reflecting the sophisticated spatial cognition of ancient Chinese military engineering. To comprehensively understand the heritage-geographical environment interaction mechanisms, this study integrates Monte Carlo simulation, spatial density analysis, kernel density estimation, and partial correlation analysis into a novel ‘Geographical Factor-Oriented Cognitive Framework for Great Wall Site Selection’. The framework deconstructs the intrinsic relationship between the Great Wall and its natural environment across three critical dimensions: spatial representation, environmental preferences, and defensive features. By systematically analyzing the interaction between individual and composite geographical factors, the research offers an innovative scientific approach to interpreting the underlying spatial logic of heritage site selection. The proposed framework is employed in a case study of the Ming Dynasty Yansui Defense District. The quantitative results indicate that the Great Wall demonstrates a significant layout strategy that combines high-density frontline defense with deep strategic support. Depending on the geographical characteristics of the eastern, central, and western routes, the siting is influenced by specific geographical combination factors, showing distinct regional characteristics: the eastern route fully utilizes the geographical advantage of numerous river valleys, with elevation and hydrographic systems being the core influencing factors, showing significant partial correlation; the central route transitions from loess ridges to desert grasslands, where visibility becomes the primary consideration for constructing the defense system; for the western route, in the loess high plain area, the elevation increases sharply, and the number of watchtowers increases, with the partial correlation of elevation and slope significantly enhanced, reflecting adjustments in defense focus and strategy. Additionally, each heritage type exhibits differentiated adaptability to geographical factors based on its specific functional characteristics, further highlighting the critical interaction between heritage siting, topography, and military strategic needs. This research provides a scientific approach to understanding the wisdom behind the Great Wall’s site selection.