The paper aims to find out the evolution of yin-yang and five elements theory and doctrine of organ manifestations under the influence of major thoughts in different ages. In Han and Tang dynasties, yin-yang and five elements were considered as qi, which came from nature. The theory of yin-yang and five elements is actually about the transformation of qi. Liver is the results of shaoyang and wood qi processes, and it stores them and then transfer them into four limbs and eyes and so on. In Tang and Song dynasties, it was believed that yin-yang is qi and five elements are its substances. They both generated from Taiji. The theory of yin-yang are the mechanism of how the universe formed. Liver is the reverting yin and wind and wood qi, which stores ministerial fire, and the flow of ministerial fire generates seminal fluid. After the late Qing dynasty, the theories were regarded as analytic devices to demonstrate diseases rather than some concrete substances. Liver is a functional body system that characterized by governing qi flow. To be specific, liver qi functions to control the flow of all kinds of qi in the body and to prevent stagnation. Also, it is believed that liver stores blood and governs qi flow, and it is a organ with yin nature but functions as a yang organ.