Muqarnas construction in Timurid architecture represents a domain in which the relationship between geometry, design, and execution can be systematically investigated. Despite prior research on the formal and decorative characteristics of muqarnas, the extent to which certain Timurid specimens conform to the historical architectural prototypes attributed to Ghiyath al-Din Jamshid al-Kashi, as well as the capacity of these prototypes to systematically explain the complex process of muqarnas generation, still requires closer examination. Aiming at a comparative study of Timurid muqarnas construction and al-Kashi’s prototypes, this research seeks to address the primary question: What correspondence exists between the geometric structure, constituent elements, and underlying geometric composition logic of selected muqarnas from this era and al-Kashi’s drafting instructions? The research methodology is descriptive-analytical with a comparative approach, in which data were gathered through library and archival studies alongside the geometric and computational analysis of selected case studies. In this study, the geometric patterns, the arrangement of components, and the relationships among constituent muqarnas units are compared with al-Kashi’s prototypes, evaluating the feasibility of articulating this process based on a rule-based logic. The results indicate a meaningful correspondence between certain examined muqarnas specimens and al-Kashi’s prototypes regarding geometric organization, component order, and shape generation; an algorithmic logic governs the design and construction of these specimens, which—in terms of generation and expansion logic—is comparable to approaches such as Shape Grammars and the Lindenmayer system (L-system). Consequently, beyond serving as mere drafting templates, al-Kashi’s prototypes provide an effective framework for understanding and explaining the structuralist logic and theoretical foundations of the design and spatial construction of Timurid-era muqarnas.