The fabrication of hybrid active sites that synergistically contain nanoclusters and single atoms (SAs) is vital for electrocatalysts to achieve excellent activity and durability. Herein, we develop a ligand-assisted pyrolysis strategy using nanoclusters (AuPd(SCHPh)) with alloy cores and protected ligands to build AuPd cluster sites embraced by satellite Pd SAs. In the thermal drive control process, different thermodynamic properties of the alloy atoms and the confinement effects of organic ligands allow for the mild spillover of the single-component metal Pd, resulting in the formation of AuPd alloy nanoclusters tightly encompassed by isolated Pd atoms. Experiments and theoretical calculations indicated that the satellite Pd atoms can optimize the electronic structure of the AuPd nanoclusters and Au sites in the alloy to facilitate the adsorption and dissociation of HO, thus enhancing the hydrogen evolution reaction (HER) activity. The optimal AuPd/Pd-600 exhibits outstanding electrocatalytic activity toward HER, with overpotentials of 21 and 38 mV at 10 mA cm in acidic and alkaline media, respectively. Moreover, the mass activity and turnover frequency of AuPd/Pd-600 are one order of magnitude higher than those of commercial Pd/C and Pt/C catalysts. This facile strategy for constructing hybrid catalytic centers using ligand-protected nanoclusters provides efficient insights for the further design of nanocluster-based electrocatalysts synergized by SAs.