To establish an ultimate energy conversion system consisting of a water-splitting photocatalyst and a fuel cell, it is necessary to further increase the efficiencies of the hydrogen evolution reaction (HER), the oxygen evolution reaction (OER), and the oxygen reduction reaction (ORR). Recently, it was demonstrated that thiolate (SR)-protected gold clusters, Aun(SR)m, and their related alloy clusters can serve as model catalysts for these three reactions. However, as the previous data have been obtained under different experimental conditions, it is difficult to use them to gain a deep understanding of the means to attain higher activity in these reactions. Herein, we measured the HER, OER, and ORR activities of Aun(SR)m and alloy clusters containing different numbers of constituent atoms, ligand functional groups, and heteroatom species under identical experimental conditions. We obtained a comprehensive set of results that illustrates the effect of each parameter on the activities of the three reactions. Comparison of the series of results revealed that decreasing the number of constituent atoms in the cluster, decreasing the thickness of the ligand layer, and substituting Au with Pd improve the activities in all reactions. Taking the stability of the cluster into consideration, [Au24Pd(PET)18]0 (PET = 2-phenylethanethiolate) can be considered as a metal cluster with high potential as an HER, OER, and ORR catalyst. These findings are expected to provide clear design guidelines for the development of highly active HER, OER, and ORR catalysts using Aun(SR)m and related alloy clusters, which would allow realization of an ultimate energy conversion system.