Phototherapy has emerged as a promising modality for cancer treatment in recent years, owing to its precise temporal control and minimally invasive nature. Here, two new organic porphyrin molecules, denoted as ONP and SNP, were designed and synthesized with an acceptor–donor–acceptor (A-D-A) architecture. The donor–acceptor (D-A) pairs in molecules facilitated the intermolecular charge transfer (ICT), thereby amplifying near-infrared (NIR) absorbance and promoting nonradiative heat generation. Notably, the substitution of oxygen atoms with sulfur in naphthalimides (NI) led to significant change of their photophysical and photochemical properties. Specifically, the sulfur atoms exhibited pronounced spin–orbit coupling (SOC) effect, leading to efficient photoinduced intersystem crossing (ISC) processes, thus facilitating the generation of reactive oxygen species (ROS). Upon self-assembly, the formed nanomaterials (ONP NPs and SNP NPs) exhibited spherical morphology with average size about 150 nm. The biocompatibility and photocytotoxicity of nanoparticles against Hepa1-6 cells were evaluated using the CCK-8 assay. Additionally, the synergistic effects (photodynamic therapy and photothermal therapy) of SNP NPs were confirmed through diverse in vitro experiment under 690 nm laser irradiation. The generation of intracellular ROS by SNP NPs was confirmed with DCFH-DA as probe. This study provides an ingenious strategy for developing organic nanomaterials with high treatment efficiency through synergistic photodynamic/photothermal effects.