Staphylococcus aureus (S. aureus) is a foodborne pathogen that endangers human health worldwide. Antimicrobial photodynamic inactivation (aPDI), mediated by titanium dioxide nanoparticles (TiO2NP), was recently used to control the growth of S. aureus, however, UV illumination had to be offered to initiate the photodynamic reaction. To overcome this drawback, a dual-photon system was established here based on TiO2NP and hypocrellin B (HB), a natural pigment with photocatalyst activity. Irradiated at the visible light (9 J/cm2) at the wavelength of 460 nm, the joint use of both photosensitizers (PS) caused a substantial decline of staphylococcal survival, reaching a maximum decrease of 4 ∼ 5 logs. When 10 nM HB and 100 µM TiO2NP were applied, a synergistic photokilling effect was achieved, only in the mixed phase of anatase/rutile, Degussa P25. Regarding the antimicrobial mechanisms, it was found that the membrane integrity of S. aureus was heavily disrupted, surface morphology was altered, intracellular substances like potassium and DNA were leaked, and biofilm formation was significantly circumvented due to the excitation of sensitized PS. In terms of antioxidant responsiveness of S. aureus, qPCR results showed that a series of genes encoding the membrane-associated cell death effectors were deregulated. Among them, LrgA was recognized as a key responsive element, due that the mutant strain harboring a constitutively-expressed LrgA strengthened the bactericidal effect of aPDI. Finally, the dual-photon strategy lowered the microbial contamination in the tested apple with its quality maintained, under the condition of visible light. Taken together, a new dual-photon system based on TiO2NP and HB was constructed and validated in photokilling S. aureus, providing a well-adapted technique to maintain food safety.