Structural transformation of high‐nuclearity nanoclusters is of significant interest because of its relevance to the formation mechanisms and stability of metal clusters. Herein, we report three large homoleptic alkynyl‐protected silver nanoclusters, [Ag ₉₈ (2‐CH ₃ C ₆ H ₄ C≡C) ₅₂ ](BF ₄ ) ₂ , [Ag ₈₆ (2‐CH ₃ C ₆ H ₄ C≡C) ₅₀ ](BF ₄ ) ₄ , and [Ag ₇₄ (2‐CH ₃ C ₆ H ₄ C≡C) ₄₄ ](BF ₄ ) ₂ , synthesized from the same precursor 2‐CH ₃ C ₆ H ₄ C≡CAg via fine‐tuning the reduction rate. X‐ray crystallography demonstrates that Ino decahedral Ag ₁₃ units serve as building blocks in all three nanoclusters. Remarkably, Ag ₉₈ undergoes an intercluster transformation in methanol. It initially converts into Ag ₇₄ , then Ag ₇₄ reacts with Ag ₉₈ to form Ag ₈₆ , which eventually is transformed into the thermodynamically stable Ag ₇₄ . Time‐dependent electrospray ionization mass spectrometry (ESI‐MS) confirms such a multi‐step reaction process during the transformation, identifying Ag ₈₆ as the key intermediate. Our findings not only provide new insights into the structural transformation pathways of nanoclusters but also enhance the understanding of transformation mechanisms, contributing to the rational synthesis of high‐nuclearity nanoclusters.

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