Unlike bulk materials, the physicochemical properties of nano-sized metal clusters can be strongly dependent on their atomic structure and size. Over the past two decades, major progress has been made in both the synthesis and characterization of a special class of ligated metal nanoclusters, namely, the thiolate-protected gold clusters with size less than 2 nm. Nevertheless, the determination of the precise atomic structure of thiolate-protected gold clusters is still a grand challenge to both experimentalists and theorists. The lack of atomic structures for many thiolate-protected gold clusters has hampered our in-depth understanding of their physicochemical properties and size-dependent structural evolution. Recent breakthroughs in the determination of the atomic structure of two clusters, [Au25(SCH2CH2Ph)18]q (q = −1, 0) and Au102(p-MBA)44, from X-ray crystallography have uncovered many new characteristics regarding the gold–sulfur bonding as well as the atomic packing structure in gold thiolate nanoclusters. Knowledge obtained from the atomic structures of both thiolate-protected gold clusters allows researchers to examine a more general “inherent structure rule” underlying this special class of ligated gold nanoclusters. That is, a highly stable thiolate-protected gold cluster can be viewed as a combination of a highly symmetric Au core and several protecting gold–thiolate “staple motifs”, as illustrated by a general structural formula [Au]a+a′[Au(SR)2]b[Au2(SR)3]c[Au3(SR)4]d[Au4(SR)5]e where a, a′, b, c, d and e are integers that satisfy certain constraints. In this review article, we highlight recent progress in the theoretical exploration and prediction of the atomic structures of various thiolate-protected gold clusters based on the “divide-and-protect” concept in general and the “inherent structure rule” in particular. As two demonstration examples, we show that the theoretically predicted lowest-energy structures of Au25(SR)8− and Au38(SR)24 (–R is the alkylthiolate group) have been fully confirmed by later experiments, lending credence to the “inherent structure rule”.