Theory of Traditional Oriental Medicine (TOM) is based on 'Yin-yang' and the 'Five elements' which are ancient chinese ideology for comprehending universe. TOM is also a kinds of ideological medicine, that contains confucian ideas, Buddhism, Taoism as progression of history and cultural trend. Ideological TOM explains physiologic and pathologic condition by 'Maintaining and Disruption of Balance' like Hippocrates, Galen, Ayurvedic medicine. The holy principle of comprehending TOM can be expressed as "To practice medicine based on ideological intuition". In western society original western ideological medicine was died out in the course of scientific revolution. But ancient and medieval oriental medicine is still in existence as a strong medical power in Korea. Recently, with the trend of academic integration, there was an attempt to find affirmative components of TOM. However, the theory of TOM is so different from any criteria for modern knowledge of science and seems to be incommensurable with modern evidence based medicine. As we know, science is the knowledge that could progress cumulatively unswayed by paradigm. To integrate TOM and modern scientific medicine, first of all, the theory of TOM must be made as a precise knowledge through strict ontological and epistemological study. The precise knowledge met clear study requirements will be integrated spontaneously, and Only that has the right to join competition for developing practical technical development. In this knowledge society, the survival and integration of TOM will not only achieved by ideological slogan but also emotional sympathy anymore.