Photodynamic sterilization is a promising alternative to conventional antibacterial approaches with merits of high efficiency and safety. The exploration of aggregation-induced emission (AIE)-type photosensitizers from natural sources is highly valued by researchers and food industry. Herein, the use of palmatine (PA), an aggregation-induced emission-active natural product from traditional Chinese medicine, as photosensitizers for photodynamic inactivation of a tenacious foodborne pathogen of Listeria monocytogenes is investigated. Antibacterial and antibiofilm activity against L. monocytogenes of PA-mediated photodynamic process were first assessed. The results showed that PA-mediated photodynamic process could inhibit the growth of L. monocytogenes, and the minimum bactericidal concentration was determined as 80 μM. At this PA dosing level, well-established biofilms of L. monocytogenes can be effectively destroyed under light irritation. Afterward, cell- and gene-level investigations were conducted to explore the antibacterial mechanism. It is concluded that the exceptional photodynamic antibacterial activity of PA against L. monocytogenes is attributed to the disruption of the cell wall and membrane, increased cell permeability, leakage of functional proteins, and damage to DNA structure. Subsequently, PA-mediated photodynamic process was applied to reduce bacterial activity in apple juice while preserving its quality. Overall, this work highlights the significant potential of PA-mediated photodynamic strategy for controlling foodborne pathogens in food systems.