In this study, we prepared photoluminescent l-cysteine (Cys)-capped gold nanoclusters (Cys-Au NCs) via NaBH4-mediated reduction of aggregated coordination polymers (supramolecules) of -[Cys-Au(i)]n-. The -[Cys-Au(i)]n- supramolecules with interesting chiral properties were formed through simple reactions of chloroauric acid (HAuCl4) with Cys at certain pH values (pH 3-7). The -[Cys-Au(i)]n- polymers could self-assemble into -[Cys-Au(i)]n- supramolecules with irregular morphologies and diameters larger than 500 nm through stacked hydrogen bonding and zwitterionic interactions between Cys ligands and through Au(i)Au(i) aurophilic interactions in solutions with pH values ≤7. The photoluminescent Au NCs (quantum yield = 11.6%) dominated by a Au13 core were embedded in -[Cys-Au(i)]n- supramolecules after NaBH4-mediated reduction. The optical and structural properties of Cys-Au NCs/-[Cys-Au(i)]n- nanocomposites were investigated, revealing that the interaction between Cys ligands plays a critical role in the self-assembly of -[Cys-Au(i)]n- supramolecules and in the formation of photoluminescent Cys-Au NCs embedded in the supramolecules. To further demonstrate that the photoluminescence properties and structures of the nanocomposites are mediated by the intermolecular forces of thiol ligands, other thiol ligands (l-penicillamine, l-homocysteine, 3-mercaptopropionic acid, and l-glutathione) and a ligand-crosslinking agent [bis(sulfosuccinimidyl) suberate; BS3] were used. We concluded that the electrostatic interactions, hydrogen bonding and steric effects dominate the polymer self-assembly into thiol-ligand-Au(i) supramolecules and thus the formation of Au NCs. Our study provides insights into the bottom-up synthesis of photoluminescent Au NCs from thiol-ligand-Au(i) complexes, polymers, and supramolecules. The hybrid Au NCs/-[Cys-Au(i)]n- nanocomposites can potentially be employed as drug carriers and bioimaging agents.