The contemporary world is characterized by an expanding network of social, cultural, economic, and technological complexities—complexities that have rendered linear and reductionist models of governance structurally inadequate and highlighted the necessity of rethinking the epistemic and methodological foundations of governing systems. Islamic civilization-building, likewise, can advance from an aspirational ideal to a programmable and operational project only when it simultaneously undertakes a reconstruction of its knowledge system and a redefinition of the relationship between Islamic sciences and the human and natural sciences, and, on the other hand, develops a model of governance compatible with the logic of complexity. This study, through a descriptive–analytical and critical approach, examines the fundamental challenges of Islamic civilization-building, the most significant of which are: (1) epistemic fragmentation and the disconnect between Islamic sciences and the modern scientific corpus, and the absence of a framework for the unity of knowledge; (2) the inadequacy of linear models in analyzing and managing the nonlinear and interwoven issues of the contemporary world; and (3) the absence of an integrated theory of Islamic governance capable of spanning from monotheistic foundations to institutional and operational design. The findings show that: (1) reorganizing religious knowledge and renewing the methodology of Islamic sciences in relation to the human and natural sciences is a necessary condition for Islamic civilization-building to enter the domain of macro-level planning; (2) Islamic governance becomes effective when monotheistic rationality, systems methodology, and an interdisciplinary perspective are coherently employed in theory production and decision-making; and (3) the proposed model of “wilāya-based governance” can, by organizing coordination across the levels of paradigm, rulings, theory, design, and implementation, provide an integrated framework for managing complexity and shaping the knowledge architecture of an Islamic civilizational project.