The principles of Islamic transcendental governance, along with the ideological-faith foundations, philosophical foundations, and value system, are the foundation of the logic of governance practice and action. Among the principles of governance are the general principles of method and structure of governance. The present article attempts, by utilizing the method of conceptual-theoretical analysis, to explore the “general methodological and structural principles” that constitute governance based on the foundations of the school of transcendental wisdom and subject them to conceptual and epistemological analysis. Therefore, the main question of the article is Based on the foundations and principles of transcendental wisdom, on what methodological and structural principles should the structure of transcendental governance be designed and institutionalized? The exploratory hypothesis of this research is that within the framework of the foundations of the school of transcendental wisdom, the methodological and structural principles of governance can be identified and formulated. The philosophical and theoretical foundation of the general methodological and structural principles of governance, the theoretical formulation of the components and structural coordinates of governance, the logic of exploring the general methodological and structural principles, and the determination of the thematic boundaries of institutional structures and their corresponding environment are among the results and innovations of this article. Also, identifying the fundamental characteristics and the standard status of the thematic dimensions of institutional structures in the environment and analyzing the fundamental nature and characteristics of the thinking and creative institution of transcendent and transcendental grassroots governance are other theoretical achievements of this article.