Human sciences in the field of understanding nature are based on specific foundations and, in the process of achieving the goals they have set for themselves, adhere to the values and rules that constitute the pillars of that knowledge and have a significant impact on the findings and applications of natural sciences and, consequently, on human happiness. On the other hand, the guidance of the Holy Quran in worldly and hereafter life necessitates a role-creating role in the field of natural sciences, the most important manifestation of which is in guiding these sciences. This research aims to reveal the role of the Quran in providing authority and guidance to natural sciences, and by utilizing the method of interrogating the Holy Quran, it has attempted to present questions received from the world of science and the activities of natural scientists to this divine book, and by describing and analyzing the relevant verses, it has attempted to answer the question of how the Holy Quran can be an authority and influence on the ontological, value-based, and teleological foundations of natural sciences. The results of this research show that the Holy Quran, by presenting a composite picture of physics and metaphysics for the universe, outlines reliable ontological foundations for natural sciences that can influence the worldview of scientists. This guidebook introduces a value system that is in harmony with reality and human happiness, and attempts to replace it with man's self-created value system, and by determining desirable goals that are in harmony with the philosophy of creation and human capabilities, directs the sciences to serve human happiness.