To develop a novel food preservation technology for efficiently enhance bactericidal activity in a long term, hollow mesoporous silica spheres (HMSS) with regular nanostructures were applied to encapsulate natural organic antimicrobial agents. The chemical structures, morphologies and thermal stabilities of linalool, HMSS and linalool-functionalized hollow mesoporous silica spheres (L-HMSS) nanoparticles were evaluated by polarimeter, field emission scanning electron microscope (FE-SEM), transmission electron microscope (TEM), fourier transform infrared (FT-IR), thermal gravimetric analyzer (TGA), nitrogen adsorption-desorption, zeta potential and small angle X-ray diffraction (SXRD). The results show that the linalool was successfully introduced into the cavities of HMSS, and the inorganic host exhibited a high loading capacity of about 1500 mg/g. In addition, after 48 h of incubation, the minimum bactericidal concentrations (MBC) of L-HMSS against Escherichia coli (E. coli), Salmonella enterica (S. enterica) and Staphylococcus aureus (S. aureus), Listeria monocytogenes (L. monocytogenes) were decreased to be 4 (< 5) mg/mL and 8 (< 10) mg/mL, respectively. These results revealed linalool-functionalized hollow mesoporous spheres could efficiently improve the bactericidal activities of the organic component. Furthermore, SEM images clearly showed that L-HMSS indeed had an extremely inhibitory effect against gram-negative (E. coli) and gram-positive (S. aureus) by breaking the structure of the cell membrane. This research is of great significance in the application of linalool in nano-delivery system as well as food industry.