Phase change heat transfer in nanoporous shape-stabilised phase change materials (ss-PCMs) is of great importance for the efficient utilization of novel energy storage materials. However, the lack of thermodynamic properties hinders the study on phase change heat transfer. In this paper, we selected the binary chloride salts (NaCl–KCl), the promising high-temperature energy storage materials for concentrating solar power, and computed their melting point using the molecular dynamics method. This study not only provides the most fundamental thermal information for the study on phase change heat transfer but reveals the mechanism of the size dependence of melting point from the aspect of the atoms. It is found that the ions in small nanoclusters vibrate more intensely and the crystal structure is easier to be destroyed, leading to lower melting point. The ion self-diffusion coefficient is also computed and analysed from the local microstructure; and it is found that the coefficient is not affected remarkably by the component and the size of nanoclusters.