In this work, we systematically investigated the ligand effect on the interface stability and the electrocatalytic performance of Au25 NCs in both the acid HER and alkaline CO2RR processes. Utilizing the hydrophilic [Au25(SCH2COOH)17] -and hydrophobic [Au25(SCH2CH3)17] -NCs as the theoretical models, we firstly explored how the ligand properties influence the Au-S interface dynamics, the electronic structures, and the electrocatalytic reaction kinetics via the constant potential calculations and ab initio molecular dynamics (AIMD) simulations. Our theoretical predictions are then validated through the experimental studies, where we synthesized the mercaptopropionic acid-protected [Au25(MPA)18] -and hexanethiol-protected [Au25(SC6H13)18] -NCs as the model systems and performed the electrochemical tests.