Of the prominent scholars who meticulously investigated in their own philosophical and interpretive works the dimensions of the subject “Velayat[1] and Caliphate” were Mulla Sadra and Imam Khomeini, both considered the great Shia thinkers. This article concerns the theo-mystical thinking of philosophers Mulla Sadra and Imam Khomeini on the issue of Velayat and the caliphate. These two thinkers have reviewed and analyzed the levels, status and typology of Velayat and Caliphate. Also, they have investigated subjects of prophethood and Imamate[2] , which are both representations of the Caliphate and Velayat. It is thus concluded that the key mystical thoughts of Imam Khomeini do not conflict with the basics of Sadr Al-Mutallehin’s Transcendental Philosophy, with the difference being that the latter has a philosophical view of the issue, and the Imam concerns with the subject by using a mystical approach.