In recent years, there were frequent exogenous contagious diseases in Eastasia like SARS(severe acute respiratory syndrome), Avian influenza, Swine influenza, MERS etc. But there are various interpretations about their pathological differentiations and lead to controversy to diagnosis and medicinal use. So there needs universal and consistent understanding methods. Several conclusions are obtained from the research on differentiation theories of various epidemic diseases. Essential elements of differential diagnostic system are pathogen, characters and matters of disease and loci, especially three yin and three yang has close affinity with constitutional features or body shape. Binding these 3 categories, an integrated differentiation 3 dimensional coordinates are made. Out of these, each elements of 3 pathogen-axial lines are related with names of exogenous disease, and those of 3 feature-axial lines are related with 8 principal patterns. And those of 3 locus-axial lines implicating therapeutic method are related with steps and location of exterior and interior, 3 yin 3 yang, Defense, Qi, Nutrient and Blood, five viscera and six bowels and tissues. Additionally, 3 lines of each axis consist of factors which have their own affinity each other, so classification of pathogen, feature, locus of disease has layered interconnectedness. This classification system is included in constitutional features of individual patient. Afterwards, these cognitive structure can be used as a general theory guiding method of therapy, prevention and aftercure healthcare.