Ternary chloride salt (NaCl–KCl–MgCl2) is considered as a potential high temperature thermal storage material owing to its low melting point, excellent thermal properties and low cost. However, the thermophysical properties of ternary chloride salts are difficult to measure under high-temperature conditions. In this study, the microscopic model of ternary chloride salt is constructed by Materials Studio software. The ratio of Na ions, K ions, Mg ions and Cl ions in the simulation system is determined according to the molar ratio of NaCl–KCl–MgCl2 eutectic ternary chloride salt. The total number of ions is identified based on computational resources and the accuracy of simulation results, and the number of the four ions in the system is finally determined. LAMMPS software is used to simulate the microstructure and calculate the thermal properties. Simulation results indicate that as the temperature increases, the distance between cluster ions increases, while the coordination number decreases, resulting in the ion association weakens. Simulation results of thermophysical properties are in good agreement with the experimental measurements. The decrease in density and viscosity is attributed to the weakening of ion association with increasing temperature. All the results are expected to provide reliable guidance for the design and preparation of next-generation concentrating solar thermal energy storage materials.