It is very important to explain the terms science, religion and metaphysics, and to explain the relation between them and also their origins. The reason for this is because all branches of knowledge are somehow related to them, or at least some of them, and they are the primary center of thought. In this paper, the deductive analytical method is used to divulge into and explain the effect these concepts have in human thought. Religion is a set of laws that organize human life, and it depends on faith, believe and inner acknowledging of religion, taking a clear ideology and acting according to it. Knowledge and understanding are the two wings of this faith and believe that are used to fly and land in the state of reality. Metaphysics is what deals and interacts with reality with analysis, and then acceptance or rejection.In this paper, we reached an important conclusion, and that is the inter-connected relation between these concepts, and there is no conflict between them, as has been claimed. Rather, one complements the other.