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Understanding the critical roles of ligands ( e.g. thiolates, SR) in the formation of metal nanoclusters of specific sizes has long been an intriguing task since the report of ligand exchange-induced transformation of Au 38 (SR) 24 into Au 36 (SR′) 24 . Herein, we conduct a systematic study of ligand exchange on Au 38 (SC 2 H 4 Ph) 24 with 21 incoming thiols and reveal that the size/structure preference is dependent on the substituent site. Specifically, ortho -substituted benzenethiols preserve the structure of Au 38 (SR) 24 , while para - or non-substituted benzenethiols cause its transformation into Au 36 (SR) 24 . Strong electron-donating or -withdrawing groups do not make a difference, but they will inhibit full ligand exchange. Moreover, the crystal structure of Au 38 (SR) 24 (SR = 2,4-dimethylbenzenethiolate) exhibits distinctive π⋯π stacking and “anagostic” interactions (indicated by substantially short Au⋯H distances). Theoretical calculations reveal the increased energies of frontier orbitals for aromatic ligand-protected Au 38 , indicating decreased electronic stability. However, this adverse effect could be compensated for by the Au⋯H–C interactions, which improve the geometric stability when ortho -substituted benzenethiols are used. Overall, this work reveals the substituent site effects based on the Au 38 model, and highlights the long-neglected “anagostic” interactions on the surface of Au-SR NCs which improve the structural stability.