All sorts of biological activities are processed thermodynamically, and at the utmost fundamental level, the laws of biology must be thermodynamics. However, the current laws of thermodynamics are unable to give reasonable explanation of biological processes. In order to do so, irreversible thermodynamics has been theorized to describe the basic mechanism for the origin of natural order or the development of things (related to developmental biology). The scientific definition of the system theory concept has been obtained and the properties of a biological system can be analyzed by applying principles of it. Irreversible thermodynamics and system theory act as the theoretical foundation for theoretical biology. By applying principles of irreversible thermodynamics and system theory, the axiomatic theory of biology has been developed.