In this research, we have simulated AgPd@Pt nanoparticles with different core structures (including the fcc, bcc, amorphous, phase-separated, and ordered structures) and different core compositions in the heating process. Our investigations showed that the phase-separated core nanocluster has higher melting temperature, and therefore, it has more thermal stability than other clusters while the bcc core nanocluster has lower melting temperature. The melting point also increases by increasing the Pd mole fraction in the cluster core. The results also showed a decrease in the configurational energy, C V , and surface energy before the melting point which is due to the diffusion of the Ag and Pd atoms to the clusters surface before the melting points. By increasing the temperature more, the different atoms of the clusters mix and form alloy structures. These results have also been approved by the radial chemical distribution function (RCDF). In order to present a complete structural investigation, the atomic strain distribution has been calculated for AgPd@Pt nanoclusters with the various core structures and compositions. The results showed that the palladium and silver atoms in the nanocluster core have more strain than the platinum atoms in the nanocluster shell. The tensile strain also exists in the cluster core, and the compressive strain exists in the nanocluster shell.