Polydopamine (PDA), CaCO3, and SiO2 were used to form a composite nano-photothermal agent (PDA@CaCO3/SiO2). Escherichia coli and Staphylococcus aureus were used as experimental strains to explore the antibacterial performance of the PDA@CaCO3/SiO2 composite nano photothermal agent on the dominant bacteria in fruits. The PDA@CaCO3/SiO2 composite nano-photothermal agent was prepared under mild conditions, and the samples were characterized using X-ray diffraction, Fourier transform infrared spectroscopy, scanning electron microscopy and Brunauer Emmett Teller analysis. The bacteriostatic effects of the PDA@CaCO3/SiO2 composite nano-photothermal agent and CaCO3/SiO2 were compared. The experimental results demonstrated the excellent photothermal conversion performance of the composite, showing a rapid temperature increase to 47.5 ℃ within 8 min. After 8 min of near-infrared irradiation at 1.2 W/cm2, the bactericidal effects of CaCO3@SiO2 and PDA@CaCO3/SiO2 on E. coli reached 90.40% and 97.34%, respectively. The antibacterial rate of the PDA@CaCO3/SiO2 composite antibacterial agent remained higher than 90% after three repeated experiments. The antibacterial test using plastic wrap containing PDA@CaCO3/SiO2 showed that the agent inhibited E. coli on the surface of fruits, with an antibacterial rate of 97.34% after 4 days of storage. The PDA@CaCO3/SiO2 composite antibacterial agent also showed good biocompatibility. This study demonstrates the antibacterial performance of the PDA@CaCO3/SiO2 composite antibacterial agent on E. coli and provides theoretical support for the research and development of biodegradable photothermal antibacterial agents in fruits.