Grasping the behavior of metal nanoclusters in solution at the atomic level is a pinnacle challenge in nanoscience. In addressing this, our work utilizes the Ag13@Ag16(BDT)12(TPP)4 (Ag29) nanocluster (where BDT represents 1,3‐benzenedithiol, and TPP is triphenylphosphine) as a template. We employ isotopic layering labeling, such as a109 Ag13@107 Ag16 core ‐shell structure, to mark the clusters. Subsequently, we conduct reactions with clusters featuring two different layering structures. Finally, we employ isotopic labeling to replace Ag in the shell, followed by analysis using ESI‐MS, enabling us to discern the process of intercluster reactions. We observed that the reactions primarily involve metal exchanges between the cores of different clusters and separately between their shells, highlighting distinct patterns of atomic‐level exchanges within these structures. This study thus offers pivotal insights into the molecular‐level mechanisms of metal exchange between clusters, significantly contributing to the development of metal nanocluster design and synthesis.