Bacteria are pivotal in the etiology of dental caries, underscoring the critical importance of effective plaque control in mitigating dental tissue diseases. Superhydrophobic materials, with their exceptional properties of non-wettability, antibacterial activity, and self-cleaning capabilities, present a promising approach for caries prevention. However, their clinical application remains constrained by challenges in achieving stable adhesion to tooth surfaces. Inspired by the natural adhesion mechanisms of acquired salivary pellicle (ASP), we synthesized Janus amphiphilic superhydrophobic nanoparticles comprising 1H,1H,2H,2H-perfluorooctyltriethoxysilane (FOTS), nano-silica, and the enamel binding peptide DDDEEKC-Peg(2000)-COOH. These nanoparticles were engineered to form a superhydrophobic film (FOTS-SiO2-Peptide) on tooth surfaces. Experimental analyses revealed rapid adsorption of these nanoparticles onto enamel, with their exposed surfaces creating a durable superhydrophobic layer that remained stable under diverse thermal conditions. Topical application of FOTSSiO2-Peptide significantly reduced the incidence and severity of dental caries while preserving oral microbiota diversity and avoiding adverse effects on surrounding mucosal tissues. Safety and efficacy evaluations confirmed the biocompatibility of these Janus nanoparticles, highlighting their potential as a novel biomedical solution for caries prevention.