The structure determination of metal nanoclusters protected by ligands is critical in understanding their physical and chemical properties, yet it remains elusive how the metal core and ligand of metal clusters cooperatively contribute to the observed performances. Here, with the successful synthesis of Au44TBPA22Cl2 cluster (TBPA = 4-tert-butylphenylacetylene), the structural isomer of previously reported Au44L28 clusters (L denoted as ligand) is filled, thereby providing an opportunity to explore the property evolution rules imparted by different metal core structures or different surface ligands. Time-resolved transient absorption spectroscopy reveals that the difference in the core structure between Au44TBPA22Cl2 and Au44L28 can bring nearly 360 times variation of excited-state lifetime, while only 3–24 times differences in excited-state lifetimes of the three Au44L28 nanoclusters with identical metal core but different ligands are observed, which is due to much stronger impact of the metal core than the surface ligands in the electronic energy bands of the clusters. In addition, the Au44 clusters protected by alkyne ligands are shown to be highly effective toward the electrochemical oxidation of ethanol, compared to the Au44 clusters capped by thiolates, which is ascribed to smaller charge transfer impedance of the former clusters. We anticipate that the study will enhance the process in controlling the nanomaterial properties by precisely tailoring metal core or surface patterns.