The position of Shiite scholars changed in different periods according to the changes that occurred in the socio-political structure of Iran, and this social group redefined and strengthened its base of influence and governance according to these developments. Therefore, the question is: Considering the comparison of the governance of Shiite scholars during the Safavid and Qajar periods, what changes did their position face, and what discourse did they prefer to strengthen their governance? This study compares the two periods using historical analysis and comparative study. It claims that Shiite scholars in the Safavid era, by getting close to the government, found "institutional" governance and were able to formulate themselves in the form of a "structure"; and by defining the "structure of governance", they achieved "governance functions". In the Qajar era, by redefining their position and independence from the government and getting closer to social forces, the clergy strengthened their social governance. They changed direction from maximum cooperation with the government to the discourse of "interaction-interaction" in this period. The Safavid era's weak "confrontational" current became extremely strong and prominent during the Constitutional Revolution. Other findings show that Shiite scholars were able to force a fundamental change in the "structure of government" and take the lead in the struggle against the unlimited "authorities" of the "sovereignty" during the Constitutional Revolution.