Molten carbonates are highly promising solar thermal storage materials. In this paper, the molecular dynamics (MD) method was used to study the thermal properties of binary molten salt mixtures of Na2CO3-K2CO3 as a function of temperature and composition. Their thermal storage mechanisms were analyzed from the perspectives of microstructure and atomic diffusion. It was confirmed that temperature and various components have significant effects on the density, thermal conductivity and shear viscosity of binary molten salts. Based upon the MD data, the correlation for the temperature-thermal properties-component with the correlation coefficient of higher than 0.98 was obtained. In addition, the radial distribution function (RDF) showed that the change in thermal properties was the result of variation in distance between the ionic clusters. Finally, based on the guidance of material composition design strategy, a coefficient that could reflect the synergistic effect between the binary molten salts was proposed for the first time. The results showed that the synergy coefficient reached its highest point for the molten salt molar ratio of 58:42, and at this point, the positive synergy was most obvious. This study can provide theoretical guidance for the design and enhancement in the performance of molten carbonates as thermal storage materials.