Reconstruction of heterogeneous catalysts during reaction, especially caused by the adsorption of reactants, is highly important for the structural evolution of nanoparticles (NPs) during activation and reaction processes. In this work, for the first time the CO-induced dynamic structure of Pd@Au core-shell NPs with different size and shape has been studied systemically using ab initio molecular dynamics. Our calculation has demonstrated that the thermostability of Pd@Au bimetallic NPs is decreased with increasing CO coverage. However, the kinetic stability can be enhanced when CO coverage is very high. With the adsorption of CO, the interaction between surface unoccupied atoms and nearby metal atoms at the second layer is strengthened, while the stress distribution in the second layer is significantly changed. The surface unoccupied metal atoms then migrate into the second layer, and metal atoms in the second layer move to surface in return. Such atomic diffusion between the top two layers leads to the atomic exchange in NPs interior layer by layer. Finally, Pd and Au atoms are redistributed in NPs, and Pd atoms accumulate at surface because of stronger CO adsorption. In a word, the segregation is dominated by the inward diffusion of surface unoccupied metal atoms. The great challenge in this work is how to establish the relationship between gas atmosphere and NP kinetic stability for determining the dynamic 3D bimetallic NPs.