Porphyrins suffer from visible light excitation, which seriously restricts photothermal therapy (PTT) to superficial lesions. Developing porphyrin derivatives with near-infrared (NIR) absorption via chemical synthesis requires complicated synthesis and purification. In this work, the electron acceptor N,N'-di(L-alanine) perylene diimide (PDI) was introduced to the electron donor tetraminophenyl porphyrin (TAPP) to prepare the charge-transfer TAPP/PDI nanoparticles (NPs) as an NIR activatable photothermal agent via a simple and efficient nanoprecipitation method. When the molar ratio of TAPP to PDI was 1:2, uniformly dispersed TAPP/PDI NPs were obtained with a new NIR absorption peak (758 nm), along with fluorescence emission quenching. These results indicated that the charge transfer from the donor to the acceptor occurred within the TAPP/PDI NPs. The co-assembly forces were proven to originate from π−π interactions and hydrogen bond interactions, according to experiment results and molecular dynamic simulation. Furthermore, the energy gap of TAPP/PDI dimer was significantly narrowed, however, the spin-orbit coupling (SOC) constant was too small for intersystem crossing, which in favor of the NIR light activated non-radiative transition of TAPP/PDI NPs. Consistent with theoretical calculations, TAPP/PDI NPs could effectively generate heat with photothermal conversion efficiency (PCE) of 36.5% under the illumination of 808 nm laser. Antibacterial experiments demonstrated that TAPP/PDI NPs could induce the death of both Gram-positive S. aureus bacteria and Gram-negative E. coli bacteria, and could eradicate S. aureus infection in mice after only one treatment. Therefore, supramolecular co-assembly affords a facile approach for fabricating NIR activated porphyrin-based photothermal agents (PTAs) for photothermal therapy and beyond.