Precise control of alloying sites has long been a challenge, yet little has been achieved in the atomic-level manipulation of metallic nanomaterials. This study reported a three-stage metal and motif exchange mechanism of alloying reaction of an atomically precise ligand-protected [Ag₄₄(p-MBA)₃₀]⁴⁻ (p-MBA = para-mercaptobenzoic acid) cluster with [Au₂(p-NTP)₂Cl]⁻ (p-MBA = para-mercaptobenzoic acid). During the first stage (Stage I), an exchange of ligand-shell metal atoms took place. During the second stage (Stage II), the motif exchanged on the [AuAg₄₃(p-MBA)₃₀]⁴⁻ cluster. During the third stage (Stage III), the Au(I) atom in the ligand-shell was swapped with a Ag(0) atom of the icosahedral Ag₁₂-core. The density functional theory (DFT) calculation results demonstrated that the metal exchange proceeded via different mechanisms at the different reaction stages. In reaction Stages I and II, the metal exchange proceeded via formation of a dianionic [Ag₄₄(p-MBA)₃₀]⁴⁻-[Au₂(p-NTP)₂Cl]⁻ intermediate and then broke and recombined with the ligand-shell. In Stage III, the diffusion of the Au(I) to icosahedral Ag₁₂-core (Stage III) was proceeded via a motif catalyzed heterometal atom diffusion mechanism. We hope that this work will provide a new perspective for the precise control of alloy position in alloyed nanomaterials.