Mosque architecture can be influenced by various factors such as culture, history, religion, geography, ecosystem, politics, and economy; therefore, a mosque cannot be considered as a uniform and abstract building, but should be examined as a phenomenological and interpretive entity resulting from the interaction between the architect, users, and the environment. Hence, examining and understanding the propositions of the mosque as one of the most important architectural, cultural, and identity symbols of Muslims becomes necessary in terms of examining and explaining the cognitive layers governing them. This research is fundamental in terms of purpose and has a combined and interdisciplinary approach. The statistical population of this research was selected and collected from available sources in reputable scientific databases in the time period of 1998-2024 in the field of mosque architecture based on purposeful sampling. For this purpose, first, the epistemological system and diverse concepts were explained based on philosophical and mystical sources, then by studying and analyzing the cognitive propositions of the mosque, categories and elements were identified that could be useful for explaining the theme of mosque architecture based on the epistemological system. In this path, the required information was collected using Attride-Stirling's thematic analysis. After confirming the validity of the codings, a qualitative model was developed. In the second step, in order to validate the qualitative model and present the final research model, the partial least squares method was used, and to examine the hypotheses created, a questionnaire was provided to 395 specialists and experienced architects based on simple random sampling, using the structural equation modeling approach. Of this number, 389 questionnaires were analyzed. The results of statistical analyses show that all relationships and paths drawn in the conceptual model are statistically significant. Therefore, it can be concluded that how the epistemological system affects mosque architecture and how these effects are manifested in various elements is the result of multilateral interaction in different cognitive layers, and understanding it correctly requires attention to all these layers. In other words, mosque architecture functions beyond merely a place of worship and social congregation, but as a cognitive and interpretive phenomenon, and through analytical and comparative methodologies, a paradigm or framework can be established for evaluating and designing a mosque based on cognitive layers.