Metal nanoclusters (NCs) exhibit potential as catalysts for electrochemical studies, providing atomic-level insights into mechanisms. However, it remains elusive to construct an integrated catalyst with a molecular-level understanding of its mechanism, especially in silver cluster assemblies. In this study, we have shown that atomically precise Ag12 cluster assemblies Ag12-py, Ag12-pyz, Ag12-bpy, Ag12-bpa, Ag12-azopy, (where Ag12 = secondary building unit, Py = pyridine, pyz = pyrazine, bpy = 4,4′-bipyridine, bpa = 1,2-bis(4-pyridyl)ethane, and azopy = 4,4′-azopyridine) serve as paradigms for demonstrating the hydrogen evolution reaction (HER), where the catalytic activity is fine-tuned using two functional units: the cluster core and the linkers. The atomic resolution of such catalysts allows tracing the reaction process via experiments coupled with theory and structural analysis. Site-specific catalysis for Ag12-pyz induced by metal cluster assembly and linker synergy can be accurately elucidated to dominate in the series. Taking advantage of the pyrazine linker due to its lower basicity and the isotropic nature of inter-cluster interactions in Ag12-pyz, it shows enhanced catalytic activity and selective hydrogen adsorption at the sulfur site, different from others in the series with nearly five times higher efficiency. This work on a series of silver cluster assemblies provides a substantial structural model to understand the catalyst’s active site and activity, further driving advancements in functional cluster-based assemblies.