The intrinsic concepts of the three yin and three yang diseases in <Shanghanlun> is unclear yet in spite of considerable controversy. In order to answer these problems, the structures of pathological transmission and anatomical terms used in the text were analyzed first. On these structural bases, the theoretical background and differential therapeutic principles of three yin and three yang disease classification. The organic structures frequently used in the text were heart, stomach, pancreas, blood chamber and urinary bladder, and the important regions in the transmission were chest, flank, epigastrium, abdomen, hypogastrium, groin on the other hand. When a host is invaded by extrinsic pathogen, an affinity is formed between the two based on the similarity of epidermal density condition and nutrient-defense features and existing disorders in the body. And then the symptoms show in 3 stages with 6 patterns in the general infective diseases. The initial stage is the period that the syndrome is limited in the external flesh area, and it mainly corresponds with taiyang bing besides the other exterior patterns of 3 yang and 2 yin bing. The middle stage is to the climax after the end of initial stage and it corresponds with mainly yangming bing including shaoyang and taiyin bing. In the terminal stage, the host gradually falls into exhaustive step or recovery phase, corresponding with shaoyin and jueyin bing. Conclusively, these dual meanings of three yang and yin should be a first guide and principle of treatment against various infective diseases.