The photochemical and photophysical properties of near-infrared (NIR) dyes are significantly influenced by their aggregation state and mesoscopic morphology. However, beyond chemical synthesis, the regulation mechanisms for the properties of NIR dyes, particularly with respect to photothermal properties of the aggregates, are not yet fully understood. Here, we investigate the photothermal behaviors of croconaine-based (CroA) NIR dyes containing dipeptide or amino acids moieties. The introduction of hydrogen bonding promotes π–π stacking of croconaine center, which can efficiently regulate aggregation states and assembly structures in isopropanol. Under laser irradiation, CroA aggregates undergo aggregation-dissociation transition, the in-situ monomer generation process regulates two parameters of photothermal performance: heating rates and plateau photothermal temperatures. This study reveals the regulation effect of non-covalent bonding interactions on CroA aggregates, highlighting supramolecular assembly strategy not only facilitates to construct of photothermal nanomaterials with well-defined structures, but also provides an alternative and effective method for regulating photothermal performance of NIR dyes.