Gold nanoclusters with precisely controlled atomic composition have emerged as promising materials for applications in nanotechnology because of their unique optical, electronic and catalytic properties. The recent discovery of a 20-gold-atom nanocluster protected by 16 organothiolate molecules, Au20(SR)16, is the smallest member in a surprising series of small gold−thiolate nanoclusters with a face-centered cubic (FCC) ordered core structures. A fundamental challenge facing gold nanocluster research is being able to understand the composition-dependent properties from a site-specific perspective in order to confidently establish structure-property relationships. A step in this direction is to examine the influence of various structural features (core geometry and thiolate-gold bonding motifs) on the bonding properties of gold-thiolate nanoclusters. In this work, ab initio simulations were conducted to systematically study the local structure and electronic properties of Au20(SR)16 from each unique Au and S atomic site using Au L3-edge extended X-ray absorption fine structure (EXAFS), projected density of states (l-DOS) and S K-edge X-ray absorption near edge structure (XANES) spectra. Two larger FCC-like gold-thiolate nanoclusters (Au28(SR)20 and Au36(SR)24) were used for a comparative study with Au20(SR)16, providing further predictions about the cluster size effect on the bonding properties of gold-thiolate nanoclusters with FCC-like core structures. Through this comparison, the smaller core size of Au20(SR)16 produces an EXAFS scattering signature that is non-FCC-like but shows very similar electronic properties with a larger FCC-like gold-thiolate nanocluster.