Semiconductor nanomaterials with photocatalytic activity have been considered as potential antibacterial materials against bacterial infection. Noble metal nanoparticles have been developed with semiconductors to promote their photocatalytic activities; however, the incorporation of noble metal NPs brings the risk of toxicity from the heavy metal species, especially for the widely used Ag nanoparticles (AgNPs). Herein, an all-organic chloridized g-C3N4/perylene-3,4,9,10-tetracarboxylic diimide (Cl-CNPD) heterostructure is chosen as a platform, in which the chloridized g-C3N4 provides bonding sites for uniform loading of AgNPs to prepare a plasmonic antibacterial nanocomposite. Benefiting from the in situ implanting approach, plasmon-induced light manipulation from the homodispersed AgNPs enables the nanocomposites to produce more reactive oxygen species (ROS), resulting in an antibacterial efficacy up to 96.1 ± 1.4% and 91.5 ± 1.8% against Staphylococcus aureus (S. aureus) under simulated sunlight (20 mW cm−2) and indoor light (5 mW cm−2) irradiation within 20 min, respectively, much higher than that of the organic heterostructure. Moreover, the strong interaction between the AgNPs and Cl-CNPD not only guarantees negligible toxicity by minimizing Ag leakage, but also shows high durability with unchanged efficacy after challenging bacteria up to five times repeatedly. Therefore, this confined plasmonic-based antibacterial nanocomposite shows great potential as a safe therapeutic system for wound disinfection.