The antibacterial efficiency and synergistic mechanisms of novel formulated eugenol entrapped ethosome nanoparticles (ELG-NPs) against fruit anthracnose were investigated. The results showed that concentrations of eugenol and ethanol significantly influenced the particle size and entrapment efficiency of nanoethosome, and the particle size significantly influenced the antibacterial effect. Superior ELG-NPs with optimized process (0.5% eugenol, 2% lecithin, and 30% ethanol) were obtained with a size of 44.21 nm and entrapment efficiency of 82%. ELG-NPs exhibited an antibacterial activity (>93%) against fruit pathogens that was greater than that of free eugenol and showed 100% inhibition of the anthracnose incidence in postharvest loquat after 6 d. The permeability study, first visualized in banana cortex with fluorescent indicators, demonstrated that eugenol delivered to the interior with ELG-NPs was 6-fold higher than that of free eugenol. ELG-NPs showed a satisfactory slow-release and prolonged antibacterial action. This work provides a promising strategy for disease controls in agricultural, food, cosmetic, and medical areas.