Electrocatalytic hydrogen evolution reaction (HER) holds promise in the renewable clean energy scheme. Crystalline Au and Ag are, however, poor in catalyzing HER, and the ligands on colloidal nanoparticles are generally another disadvantage. Herein, we report a thiolate (SR)-protected Au36Ag2(SR)18 nanocluster with low coverage of ligands and a core composed of three icosahedral (Ih) units for catalyzing HER efficiently. This trimeric structure, together with the monomeric Ih Au25(SR)18- and dimeric Ih Au38(SR)24, constitutes a unique series, providing an opportunity for revealing the correlation between the catalytic properties and the catalyst's structure. The Au36Ag2(SR)18 surprisingly exhibits high catalytic activity at lower overpotentials for HER due to its low ligand-to-metal ratio, low-coordinated Au atoms and unfilled superatomic orbitals. The current density of Au36Ag2(SR)18 at -0.3 V vs RHE is 3.8 and 5.1 times that of Au25(SR)18- and Au38(SR)24, respectively. Density functional theory (DFT) calculations reveal lower hydrogen binding energy and higher electron affinity of Au36Ag2(SR)18 for an energetically feasible HER pathway. Our findings provide a new strategy for constructing highly active catalysts from inert metals by pursuing atomically precise nanoclusters and controlling their geometrical and electronic structures.