Using molecular dynamics (MD) simulation, the thermal efficacy of phase change materials (PCMs) in solar energy applications and solar thermal energy storage was evaluated. In order to achieve this objective, an investigation was conducted into the structure's temperature (Temp), velocity, and density profiles, heat flux, thermal conductivity, charge and discharge time, and thermal stability. Three models of tube, shell, and shell-tube were adopted to scrutinize the atomic behavior and thermal performance (TP) of PCMs. The results show that the maximum density of the tube model, shell model, and shell-tube model was 0.042, 0.036, and 0.033 atom/A3, respectively. Other numerical results showed that the maximum velocity for the three structures of tube model, shell model, and shell-tube model under the initial Temp of 300 K was 0.0066 Å/fs, 0.0059 Å/fs, and 0.0054 Å/fs, respectively. The structure in the tube model manifested more optimal atomic behavior compared to other models. The TP of simulated structures revealed that the heat flux of the samples reached 5.69, 4.85, and 4.15 W/m2, respectively. Finally, the thermal conductivity of the structures approached 1.35, 1.32, and 1.31 W/m.K, respectively. The results suggested that the tube model had the most thermal stability and showed the optimal thermal behavior in the simulation. The findings of this study, particularly the optimal atomic behavior and thermal stability of the tube model, can be useful in designing and optimizing PCMs for solar energy applications. In general, this research had the potential to significantly advance the field of solar energy system efficiency and cost-effectiveness.