The concept of entropy and its relevant principles, mainly the principle of maximum entropy production (MEP), the effect of negative entropy flow (NEF) on the organization of atmospheric systems and the principle of the Second Law of thermodynamics, as well as their applications to atmospheric sciences, are reviewed. Some formulations of sub-grid processes such as diffusion parameterization schemes in computational geophysical fluid dynamics that can be improved based on full-irreversibility are also discussed, although they have not yet been systematically subjected to scrutiny from the perspective of the entropy budgets. A comparative investigation shows that the principle of MEP applies to the entropy production of macroscopic fluxes and determines the most probable state, that is, a system may choose a development meta-stable trajectory with a smaller production since entropy production behavior involves many specific dynamical and thermodynamic processes in the atmosphere and the extremal principles only provide a general insight into the overall configuration of the atmosphere. In contrast to the principle of MEP, the analysis of NEF is able to provide a new insight into the mechanism responsible for the evolution of a weather system as well as a new approach to predicting its track and intensity trend.