To reduce the deterioration of fruits and vegetables caused by food-borne microorganisms, this study proposed a bio-sustainable PCD-CS photothermal bactericidal nanocomposite film. This film integrated L-Cysteine (L-Cys) coated polydopamine nanoparticles (PDA@L-Cys NPs) and deep eutectic solvents (DES) into the chitosan (CS) matrix. The DES effectively improved the mechanical property of composite film, water vapor barrier property (WVP), transparency, and biodegradability. The inclusion of PDA@L-Cys NPs significantly increased the oxidation resistance, UV-shielding, and photothermal conversion capabilities. The oxidation resistance of composite film improved 3–7 times compared to the bare CS film. Under near-infrared irradiation (NIR) for just 10 min, the temperature of the film can rise to 55.8 ℃, achieving a photothermal antibacterial rate reached 99.9% against Escherichia coli (E. coli, ATCC 8739) and Staphylococcus aureus (S. aureus, ATCC 6538). Under single short-time NIR trigger, the PCD-CS nanocomposite film effectively maintained good color, pH value, soluble solid content (TSS), and appearance of cherry tomato, and delayed the decrease of weight. The successful implementation of this work provides new insights and approaches for creating and advancing sustainable antibacterial food packaging.