Thermal energy storage materials are carriers of thermal energy. The physical and chemical properties of these materials dictate their thermal storage performance. Accurate modeling of them under both ideal and industrially relevant conditions is valuable in terms of predicting influences of materials properties on device and system level performances, and understanding potential constrains and methods for overcoming the limitations of the materials. Recent years have seen the development and applications of new composite materials for thermal energy storage, which bring difficulties to the modeling of these materials. Examples include the strong scale effect due to the doping of nanoscale particles to thermal storage materials. Therefore, microscopic modeling is needed for in-depth understanding of these phenomena. In this chapter, density functional theory (DFT) and molecular dynamics (MD) methods are introduced in detail for modeling thermal energy storage materials from a microscopic aspect.