Ligand exchange reactions can introduce new ligands onto clusters to afford new physical/chemical properties and functions. Many studies on the ligand exchange reactions of thiolate-protected gold clusters using other chalcogenates (i.e., selenolates or tellurolates) as exchange ligands have been conducted in recent years. However, there is limited information on the preferential exchange sites and electronic structure of the exchanged products. In this study, we investigated the geometric and electronic structures of the products obtained by reacting [Au-25(SC2H4Ph)(18)] with PhSeH or (PhTe)(2) by single-crystal X-ray structural analysis, differential pulse voltammetry, and optical absorption spectroscopy. The results revealed that these exchange reactions preferentially produce products containing substituted ligands close to the gold core. In addition, we quantitatively determined the changes in the redox potentials and optical transition energies induced by continuous ligand exchange. This systematic investigation revealed that exchange with SePh induces nonlinear changes in the electronic structure of the clusters with the number of exchanged ligands. These findings are expected to lead to the improved design guidelines to produce clusters with new functions by ligand exchange with other chalcogenates.