The formation of a widespread Safavid Shiite government in Iran made possible serious changes in the relationship between religion and government in Shiism. Clergymen as the main part of religious sect encountered a special and historical situation. The decision on how to interact with Safavids was very fundamental and strategic. Safavids themselves faced a great challenging and complicated situation in establishing a relationship with religious sect, because the principles of Shiism could challenge the government's legitimacy. The present study, through official records and other documentary materials, tries to reinterpret the complications of the interaction the two sides experienced and to open a new perspective for analyzing this historical phenomenon (event). The base of the analysis of the present study is to take into account a sort of conflict and disagreement in the interaction between clergymen and Safavids.