Phase change material (PCM) is a material that has a specific melting point, and its latent heat of melting is large enough that it can be used to store thermal energy. This study investigated the effect of size (4–8 Å), and the number of layers (3–10 layers) of iron nanoparticles (NPs) channel on thermal behavior (TB) and phase change (PC) process of sodium sulfate/calcium chloride hexahydrate (Na2SO4/MgCl2·6H2O) PCM molecular dynamics (MD) simulation. By increasing the number of layers from 3 to 5, the maximum temperature and heat flux (HF) increased from 406 and 1471 W/m2 to 451.51 K and 1496 W/m2. By increasing the number of layers from 3 to 7 layers, the charging time (CT) and discharge time (DT) of atomic samples decreased from 4.01 ns and 4.25 ns to 3.88 ns and 4.17 ns. By adding the iron NPs with a radius of 4, 5, 6, and 8 Å, the maximum temperature increased to 420, 429, 458, and 503 K, respectively. By adding the iron NPs with different radii from 4 to 8 Å, the HF inc