In all periods of brilliant Gnostic heritage of Islam, much has been written about esoteric meanings and secret depths of the Qur'an and traditions. Numerous representatives of Muslim practical and doctrinal gnosis have extensively interpreted the most sophisticated teachings of sacred religious texts revealing them in the light of their intuitive knowledge of the human's soul path of development, and the highest realities of the metaphysical sphere of existence. In this paper, we first determine the basic historical contexts and terminology of the process of Gnostic hermeneutics of Islam, and then we extensively analyze the most important ontological-anthropological and methodological principles of the process. As the aforementioned rational principles have been elaborated on in an established demonstrative-philosophical language in the school of transcendental philosophy - the most dominant traditional philosophical school of Islam, we will use here primarily the method of detailed analysis of the contents of the most influential works of the renowned founder of the school, Mulla Sadra Shirazi. We show that the esoteric depths of the primordial Qur'anic messages are recognized in the same way that the existence of numerous profound spheres of the entire universe and human beings is established. We will also explain that in the process of hermeneutic discovering of layered secrets of the Qur'an and traditions, Muslim Gnostics do not reject the exoteric meanings of Qur'anic message, but they deepen these meanings, freeing them from unnecessary restrictions of material forms and thus reach the essential mystery of God's speech.