The present article studied the nature and foundations of the theory of "Three-layer interpretation of the Holy Qur’an". First, the theory is defined, consisting three layers: historical, trans-historical and modern. The historical layer is considered the same understanding of Hejaz Arab at the time of the Prophet (PBUH) as stated in the verses of the Qur'an. To understand such interpretation, one must refer to the promises of those people, some of which are the appearance and context of the verses, similar verses, the personality of the audience of the Qur'an, the events of that era, the culture and history of those people and the covenants. The trans-historical layer is also considered a knowledge that is common and accepted among all human races, which is achieved by abolishing the characteristics of the age and the revelation of the Qur'an. The modern layer is the adaptation of the problems, that needs and requirements of the present age to the same common and acceptable human knowledge. Some of the most important foundations of this theory that are discussed in this article are customary, spoken, gradual descent, historicity and marginalization on the one hand and the evolution of ethnic requirements and the need to resolve the apparent conflict between the Qur'an and science and modernity.