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Extensive recent efforts have been put on the design of high‐performance organic near‐infrared (NIR) photothermal agents (PTAs), especially over NIR‐II bio‐window (1000–1350 nm). So far, the development is mainly limited by the rarity of molecules with good NIR‐II response. Here, we report organic nanoparticles of intermolecular charge‐transfer complexes (CTCs) with easily programmable optical absorption. By employing different common donor and acceptor molecules to form CTC nanoparticles (CT NPs), absorption peaks of CT NPs can be controllably tuned from the NIR‐I to NIR‐II region. Notably, CT NPs formed with perylene and TCNQ have a considerably red‐shifted absorption peak at 1040 nm and achieves a good photothermal conversion efficiency of 42 % under 1064 nm excitation. These nanoparticles were used for antibacterial application with effective activity towards both Gram‐negative and Gram‐positive bacteria. This work opens a new avenue into the development of efficient PTAs. [ABSTRACT FROM AUTHOR]