Agha Bozorg Mosque is the only 5-story mosque in the world known as one of the masterpieces of Qajar period architecture. In addition to “Sunken Courtyard” architecture and wind towers, this construction observes the quadruple principles of Islamic architecture as well. The quadruple principles of Islamic architecture consist of decorative artifacts including Muqarnas (a form of ornamented vaulting in Islamic architecture), Girih (a decorative Islamic geometric artform used in architecture and handicraft objects, consisting of angled lines that form an interlaced strapwork pattern), Yazdi-Bandi and Rasmi-bandi. The portal, the central courtyard, 3 Shabestans, and Gonbad-khaneh are the main sections of this mosque.
Agha Bozorg Madrasah (Theological school) also includes 12 chambers, which were used in the past by theologies to learn religious teachings.