In this study, Pt@Au core-shell nanoparticles were simulated by a classical molecular dynamics method to investigate the influences of morphologies of the core and shell regions on structural stability and melting behavior of these nanoparticles. For this aim, the nanoclusters with the same shell and different cores including rattle-core, porous-core, and dense-core types were considered. Through investigation of the shell effect, nanoclusters with the same core and different shells including dense-shell, continuous porous-shell, and discontinuous porous-shell were selected. The data for simulations were analyzed by potential energy, heat capacity, excess energy, deformation parameter, common neighbor analysis, and radial distribution function methods. The results indicated that dense-core and dense-shell nanoclusters exhibit the highest thermodynamic stability and melting point. Among various core morphologies, porous-core, and among various shell structures, the discontinuous porous-shell structure showed the lowest thermodynamic stability. The results indicated that melting starts from the shell region, and there is a considerable tendency for Pt atoms in the core to mix with Au atoms in order to create a mixed alloy at higher temperatures. This result implies the instability of core/shell regime at high temperatures.