Contemporary studies largely concentrate on the physical aspects of architecture, yet within the sphere of design, the gap between user experience and the designer’s intention is an undeniable fact. This gap, illustrating the contrast between the spatial perception and the actual physical space, to some degree, mirrors preferences in human spatial behavior. It accentuates the complex relationship between human cognitive functions and spatial layout, underlining the critical role of spatial perception in architectural design and planning. This prompts the question of whether perceptions of internal traffic flow within buildings also suffer from spatial distortions. Focusing on museums, and by examining circulation paths and spatial features, a virtual museum model is devised. The research employs a holistic and reductionist approach (complex systems theory) to forge a link between circulation components and the spatial experience of architecture. Utilizing agent-based modeling tools for simulating pedestrian movements, it investigates how different circulation patterns and spatial relationships influence pedestrian behavior. The study proposes a museum circulation optimization strategy, grounded in quantifying spatial experience through Anylogic software analysis. This strategy is aimed at enhancing the design of internal traffic flows in future museum projects, offering fresh insights into museum design research, and probing into new possibilities for using pedestrian simulation software.