Using ligand-protected metallic nanoclusters with atomic precision as catalysts and elucidating its ligand effect in the catalysis are the prerequisites to deepen the structure-catalysis relationship of nanoclusters at the molecular level. Herein, a series of Ag33 nanoclusters protected with different thiolate ligands (2-phenylethanethiol, 4-chlorobenzyl mercaptan, and 4-methoxybenzyl mercaptan as precursors) were synthesized and used as heterogeneous catalysts for the conversion of nitroarenes to arylamine with NaBH4 as reductant. The obtained nanoclusters exhibited ligand-dependent catalytic activity, with benzyl thiolate ligands distinctly superior to the phenethyl thiolate ligands. DFT calculations revealed that the ligand regulated catalytic activity of the nanoclusters was ascribed to the H-π and π-π interactions between the ligands and the substrates, owing to the presence of phenyl rings in these structures. This work highlighted the importance of the ligands on the metallic nanoclusters in catalysis and provides a strategy to regulate the catalytic activity by utilizing weak interactions between the catalysts and the substrates.