The impact of interfacial charge on catalytic performance of supported-metal-cluster (SMC) heterostructures remains unclear, hindering efforts to develop high-performance SMC catalysts. Herein we systematically investigated interfacial charge effects of SMCs using a model system of graphene-supported gold-nanoclusters (AuNCs/rGO) for azo hydrogenation. Three types of SMCs with different interfacial charges were synthesized by anchoring electropositive 2-aminoethanethiol (CSH), amphoteric cysteine (Cys), and electronegative 3-mercaptopropionic-acid (MPA) onto AuNCs/rGO, respectively. All three SMCs exhibited high and selective catalytic activity to azo-hydrogenation in four representative azo dyes. The catalytic activity of Cys@AuNCs/rGO was lower than that of CSH@AuNCs/rGO but higher than that of MPA@AuNCs/rGO. However, the cyclic stability of Cys@AuNCs/rGO was inferior to that of both CSH@AuNCs/rGO and MPA@AuNCs/rGO. Further mechanistic studies revealed that amino ligands modified CSH@AuNCs and Cys@AuNCs agglomerated into large-size gold nanoparticles on rGO surface during catalytic reaction under NaBH₄ action, leading to reduced efficiency and cyclic stability. Conversely, non-amino ligand modified MPA@AuNCs only partially detached from rGO surface without agglomeration, resulting in better cyclic stability. Protection of amino groups in ligands such as modifying –NH₃⁺ group in Cys into imine to form N-isobutyryl-L-cysteine (NIBC) substantially improved the cyclic stability while maintaining the high activity in the NIBC@AuNCs/rGO catalyst system. Our work provides an approach for developing a highly-active and stable SMC heterostructure catalyst via manipulating interfacial charges in SMC.