To achieve targeted clearance of bacteria and their biofilms, a straightforward strategy to integrate antimicrobial alternating polymers with photothermal polydopamine nanoparticles (PDA NPs) is proposed. By manipulating the alternating distribution of electrostatic, hydrophobic, and hydrogen bonding units in the polymer backbone, the thermal stability of polymer‐particle interaction can be tuned, enabling photothermal‐mediated in situ delivery of cationic antimicrobial polymers into bacteria. The alternating polymer coating significantly enhances the penetration capability of NPs into the Methicillin‐resistant Staphylococcus aureus (MRSA) and Escherichia coli (E. coli) biofilm, achieving a 99% bactericidal rate within the biofilm at a low concentration after 10 min of near‐infrared irradiation, whereas pristine PDA NPs shows negligible effects. The in‐vitro co‐culture model demonstrates that alternating‐polymer‐loaded NPs selectively eradicate 1 × 107 CFU mL−1 of MRSA and E. coli while preserving over 75% viability of the mammalian cells, including mice fibroblasts, human kidney cells, human cervical cancer cells, and macrophages. The efficacy of these biocompatible NPs in targeting bacteria is further validated in a mouse MRSA‐infected wound model. This approach represents a significant advancement in developing safe and efficient antimicrobial therapies with targeted bacterial killing and minimal off‐target effects based on alternating cationic polymers.