since the government, following the Shi’ie doctrine, paid special attention to art and architecture, the School of Isfahan found the opportunity to manifest the Shi’ite beliefs in architecture. The rare combination of art, Shi’ism and illumination gave this era a unique identity, which manifested itself more or less in the Isfahan school of art and architecture. Shia influence in the political and mental system for the first time in this era, provided the best situation for mental growth and merger of intellectual and religious currents based on Shia ideology. This paper deals with one of the principles governing the organization of art and architecture with the aim of re-examining the role of thought currents dominant at the Safavid era in architecture. The principle of hierarchy in architecture represents the effort to express the concept of transition and the gradual cognitive process. In traditional arts, this has been known as one of the basic principles. The mosque represents the most salient manifestation of this principle in architecture, which is related to the cognitive aspects of space. In particular, the entrance of the mosque as a place linking the worldly and the heavenly finds a celestial dimension, which prepares the person, through a cognitive process, for a transition from the material to the spiritual. The most salient instance of this principle in the architecture of mosques is the intelligent increase of spatial ranks. In this paper pursuing the principle of hierarchy in Iranian-Islamic thought, Mola Sadra Shirazi and illumination sheikh Sohrevardi ideas -that influences in art and architecture of this era- were investigated the evolution of these ideas in the design of mosques as a finest traditional art. With access the basic connection between this principle and Shiite, mystical and illumination though, were obtained the noticeable field for deeper analysis of the samples. A comparison of the facades of the mosques built in the era under study, the era when the school of Isfahan emerged, with previous facades, shows the following results: 1-A considerable increase of spatial ranks in the facades of the mosques built in the Safavid era, a characteristic which continues in a number of succeeding mosques As one of the most important results of this study. 2-A new method developed in the making of the entrance space of the mosques built in this era, used for the first time in the entrance space of the Shah Mosque in Isfahan. 3-The School of Isfahan has drawn the attention to the transition from without to within. The increase of the entrance ranks of the mosques explains the process of preparing the person coming to the mosque to say prayers to transit from the material to the spiritual. 4-The hierarchy principle, a major principle of architecture in the Shi’ite world, employed in the creation of architectural space is closely tied to the Shi’ite doctrine and the related concepts. A re-examination of this principle and intelligent application of it in modern architecture with no doubt would promote the structure and semiotics of architecture.