The aim of this article is to explain the transformations experienced by the religious institution in Iranian society, drawing upon the framework of complexity theory. Using an analytical approach and literature review, the study examines the religious institution as a complex and dynamic system characterized by features such as non-linear behavior, self-organization, and the emergence of novel properties. The findings indicate that, following the Islamic Revolution, the religious institution in Iran ascended from the status of a sub-system to that of a dominant institution within the social structure; however, this elevation has been accompanied by fundamental challenges. Analysis at the macro, meso, and micro levels reveals that factors such as rising educational attainment, urban expansion, and changes in the processes of religious socialization have been the primary drivers of these transformations. Additionally, the emergence of new and unpredictable forms of individualistic and autonomous religiosity—shaped by the dynamics of complex systems—stands out as another significant result of this research. Accordingly, it is projected that the future trajectory of Iran's religious institution will depend on its adaptive capacity, internal dynamism, and self-renewing power, enabling it to maintain cohesion and play a constructive role within society.