Improving the fundamental understanding of the basic structures of ligand‐protected gold nanoclusters is essential to their bottom‐up synthesis as well as their further application explorations. The thiolate ligands that cover the central metal core in staple motifs are vital for the stability of the gold clusters. However, the knowledge about the geometrical and bonding characters of the thiolate ligands has not been fully uncovered yet. In this work, density functional theory calculations and molecular orbital analysis are applied to show that the Au atoms in the thiolate ligands are hypervalent. The chemical insights of the linear SAuS configuration as well as the lengthened AuS bond by combining the 3‐center 4‐electron (3c‐4e) model and the well‐recognized valence shell electron pair repulsion theory are revealed. Valence bond formulations of the motifs are given to provide more chemical insights, for example, the resonant structures, to show how the thiolate motif forms one covalent bond and one dative covalent bond with the Au core. This work provides a thorough understanding of the structure and bonding pattern of thiolate ligands of Au nanoclusters, which is important for the rational design of ligands‐protected Au nanoclusters.