Precise control of alloying sites has long been a challenging pursuit, yet little has been achieved for the atomic-level manipulation of metallic nanomaterials. Here we describe utilization of a surface motif exchange (SME) reaction to selectively replace the surface motifs of parent [Ag₄₄(SR)₃₀]^4- (SR = thiolate) nanoparticles (NPs), leading to bimetallic NPs with well-defined molecular formula and atomically-controlled alloying sites in protecting shell. A systematic mass (and tandem mass) spectrometry analysis suggests that the SME reaction is an atomically precise displacement of SR-Ag(I)-SR-protecting modules of Ag NPs by the incoming SR-Au(I)-SR modules, giving rise to a core-shell [Ag₃₂@Au₁₂(SR)₃₀]^4-. Theoretical calculation suggests that the thermodynamically less favorable core-shell Ag@Au nanostructure is kinetically stabilized by the intermediate Ag₂₀ shell, preventing inward diffusion of the surface Au atoms. The delicate SME reaction opens a door to precisely control the alloying sites in the protecting shell of bimetallic NPs with broad utility.