Gold (Au) clusters with well-defined geometrical structures have attracted substantial attention due to their unique optical and catalytic properties, which are drastically changed by the ligands, compositions, and geometric structures. Here, we investigated the effect of ligand on the electronic state of Au in [Au9(PPh3)8]3+ (Au9) and [Au25(SC2H4Ph)18]- (Au25) by X-ray absorption spectroscopy using high energy resolution fluorescence detection (HERFD) and theoretical calculations. Au L3-edge X-ray absorption near-edge structure (XANES) spectra revealed that the white-line intensity of Au9 was comparable to that of Au25, while the white-line peak of Au25 was 3 eV lower than that of Au9. The total area of the white line of Au9 corresponded to that of Au25, which is explained by the natural bond orbital analysis, showing that the occupancy of Au 5d orbitals of Au9 was close to that of Au25. The simulated XANES spectra using finite difference method near-edge structure software resembled the experimental XANES spectra. The projected density of state profiles and molecular orbitals indicated that the unoccupied 5d orbitals of the surface Au in Au9 and of surface and oligomer Au in Au25 interacted with P/S 3s+3p orbitals. The difference in peak locations in Au L3-edge XANES between phosphine- and thiolate-protected gold clusters was ascribed to the energy shift of unoccupied Au 5d orbitals, which are modulated by the Au 5d and P/S 3s+3p interaction.