Understanding the assembly pattern of metal nanoclusters in crystalline units at the atomic level is crucial for an in-depth understanding of their supramolecular interactions and structure–property correlations. In this study, two Au₉Ag₆ nanoclusters bearing a similar framework were controllably synthesized and structurally determined. By tailoring the peripheral thiol ligands from SPh^pOMe to SPh^oMe (HSPh^pOMe = 4-methoxythiophenol, HSPh^oMe = 2-methylbenzenethiol), the hierarchical assembly of cluster molecules in their superlattice varied from “ABAB” to “ABCDABCD”. Based on the atomically precise structures of the two nanoclusters, we proposed that such differences in crystalline packing modes resulted from a combination of their structural differences, including intramolecular coordination preferences (Au–P vs. Ag–Cl), steric hindrance effects of thiol ligands (SPh^pOMe vs. SPh^oMe), and intra-/inter-cluster interactions (C–H···π, π···π, and H···H). We also investigated the structure/assembly-dependent optical properties of the two clusters at different states and rationalized the obtained structure–property correlations at the atomic level. Moreover, this study presented an interesting case for analyzing the hierarchical assembly of metal nanoclusters, allowing an in-depth understanding of the ligand effect on the crystalline assemblies of metal nanoclusters with atomic precision.