Au@void@AgAu yolk-shell nanoparticles with different morphologies were studied by classical molecular dynamics simulation. The results indicated that all of simulated yolk-shell nanoclusters with ∼3.8 nm size and different morphologies are unstable at room temperature, and collapse of the shell atoms into the void space completely fills it and creates more stable Au@AgAu core-shell structures. Also, it was observed that thermodynamic stabilities of the created core-shell structures strongly depend on the morphology of nanocluster, for which competition between strain and surface energy effects plays the key role in this phenomenon. Within this competition, strain effect is dominant and helps the stability of the created core-shell structure. Herein, the icosahedral nanocluster with the lowest strain effect exhibits the highest thermodynamic stability. By comparing the simulation results with experimental data, it was concluded that the essential factor that controls the stability of these nanoparticles is their size. © 2017 American Chemical Society.