Domesticating human sciences has always been one of the concerns since the Islamic Revolution of Iran, regarding to its hidden values, which can strengthen the process of identity-making in the political system. The key point here is the Islamic meta-theories which pave the way for other theories, approaches, and even various tactics, especially in the defense and foreign policy issues. Every theory possesses its own meta-theory which forms them and highlights their fundamental principles. Three variables are also significant in metatheories, including ontology, epistemology, and anthropology. They, in fact, determine how to perceive the world and how to look at man and the philosophy of its being. In order to understand, explain, and prescribe the security standpoint of the IR of Iran, it is required to study the ontology of the IR of Iran profoundly. This paper studies the ontology of the security school of the IR of Iran. It proposes that this security school places a premium on the non-materialistic, identity-related, and software factors rather than on the physical, materialistic, and hardware factors. In this security school, spiritual and identity-making factors are hugely important to the point that they form a border between self and the other.