Thiolato-protected gold nanoclusters have acquired wide applications; however, on the fundamental science end there is still a lack of deep understanding of their high stability. Recent success in transforming the highly robust biicosahedral Au38(SCH2CH2Ph)24 nanocluster into an extremely stable tetrahedral Au36(SPh-(t)Bu)24 nanocluster raises an important question: Is the transformation due to the bulkiness effect of SPh-(t)Bu or the electronic conjugation effect of the aromatic ligand as opposed to the nonaromatic SCH2CH2Ph? Toward this goal, we report our success in the crystallization of a nonaromatic thiolato-protected Au36(SC5H9)24 nanocluster (where, SC5H9 = cyclopentanethiolato). Comparison of Au36(SC5H9)24 with the aromatic thiolato-protected Au36(SPh-(t)Bu)24 nanocluster rules out the thought that the face-centered cubic, tetrahedral structure of Au36(SPh-(t)Bu)24 is dictated by the aromatic ligand; it also reveals that the electronic conjugation effect in aromatic ligand makes the S-C bond shorter and stronger, and this affects the S-Au bonds, resulting in a larger separation between the staple motifs and the inner Au28 kernel. Overall, this work sheds some light on the major question of the specific roles of thiol ligand in determining the cluster size and structure.