The nanostructuration of Ag thin films deposited on the MgO(100) substrate is simulated by classical molecular dynamics using a tight-binding many-body potential for the metal-metal bonds and a potential fitted to ab initio calculations for the metal–oxide ones. Due to the lattice mismatch between the Ag deposit and the MgO(100) substrate, the silver film is strained. The stress is partially released by the introduction of misfit dislocations at the interface. These dislocations form a network with a periodicity of about 10 nm, which varies for ultrathin films according to the film thickness. The strain induced by the interfacial dislocation cores propagates across the silver film up to the surface driving to the nanostructuration of the surface. The atomistic results are compared to the predictions of the elasticity theory. The theoretical results are in a nice agreement with recent experiments obtained by grazing incidence small angle x-ray scattering revealing a self-organization of Co clusters adsorbed on a thin film of Ag/MgO(100) [F. Leroy, G. Renaud, A. Letoublon, R. Lazzari, C. Mottet and J. Goniakowski (unpublished)]. We show that the preferential Co adsorption site is obtained on top of tensile surface sites and that the periodicity of the clusters' self-organization can be tuned by the Ag film thickness.