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Bimetallic nanoparticles (NPs) have become one of hot spots in materials science due to their unique physical and chemical properties. The alloying process of core-shell structured Ag-Au NPs has been investigated with a modified analytic embedded atom method (MAEAM) and molecular dynamics. The influence of shell thickness on alloying behavior has been studied from the viewpoint of atomic diffusion, microstructure evolution and alloying extent. For NPs with a thin shell, there is a significant atomic diffusion at the core/shell interface. The Ag core undergoes a shape evolution from initial spherical to polyhedron. The surface Au and Ag atoms are fully mixed. For NPs with a thick shell, the atomic diffusion is mainly located to the surface of NPs. The NPs exhibit polyhedron morphology with the Ag core almost unchanged. The morphology above is changed through the stacking fault growth. Compared with the thick shell, the alloying extent of NPs with a thin shell is much greater