Waterborne diseases caused by pathogenic microorganisms pose severe threats to human health. ZnO nanoparticles (NPs) hold great potentials as an effective, economical and eco-friendly method for water disinfection, but the exact antimicrobial mechanism of ZnO NPs under visible-light illumination is still not clear. Herein, we investigate the visible-light-driven photocatalytic inactivation mechanism of amino-functionalized hydrophilic ZnO (AH-ZnO) NPs against Staphylococcus aureus (S. aureus) in aqueous environment from the perspective of electron transfer theory. The results show that the antibacterial effects of AH-ZnO NPs are dependent on the AH-ZnO NPs concentration and treatment time. The bulk ORP value and released Zn2+ concentration in AH-ZnO NPs solutions increase with AH-ZnO NPs concentration. The SEM and intracellular protein leakage results indicate that AH-ZnO NPs can adhere to S. aureus surface without causing obvious cell membrane disruption. The photoluminescence (PL) intensity and fluorescence lifetime of AH-ZnO NPs are remarkedly decreased after adding S. aureus, which confirms the electron transfer from S. aureus to AH-ZnO NPs. Moreover, the ΔPL intensity is closely correlated with the inactivation efficiency, demonstrating that the interfacial electron transfer in S. aureus/AH-ZnO NPs composites contributes to the antibacterial activity, which is speculated to disrupt the normal respiratory electron transfer chain of S. aureus, thereby causing intracellular ROS generation, cell membrane depolarization and eventually apoptosis-like death.