The thermodynamic principles for system biology are reviewed and formulated, and then basic patterns of flower pigmentation are interpreted. Main thoughts: (1) any biological trait (color or function of a cell) is logically related to a thermodynamic system (or physiological system, signaling network of the cell), (2) the striped, speckled and circle are three basic patterns of flower pigmentation, the development of flowers is an irreversible process, (3) the patterns of flower pigmentation are formed in flower development, (4) the flower cells can change its color in a period of development and this process is controlled thermodynamically, (5) there is giant space of physiology within an organism and within its numerous thermal states can appear under different conditions. In this theory, the dominant inheritance means that a gene contributes great to the thermodynamic stability of a trait related system; different genes can be interacted or integrated thermodynamically according to their contribution to the stability of its related system. By combination of Turing theory and our views, complex patterns of pigmentation could be explained theoretically.