Here, we firstly designed an advanced PTA, probe-1, based on a special D− π − A structure with strong NIR absorption near 800 nm. It is successfully dispersed into water and endowed with targetability for tumors by loading into hydrogel to form nanoparticles, probe-1-cRGD. However, the absorption peak (λmax) of probe-1-cRGD blue-shifted to 690 nm because the strong antiparallel aggregation, which deviated from the ideal 808 nm excitation. To optimize the photothermal performances at 808 nm after loading to hydrogel, we further constructed another PTA, probe 2, by changing the non-conjugated substituents to regulate its aggregation behavior. The experimental data shows that both probes possess high PTCEs (60.5% and 57.3%) and that probe-2-cRGD exhibits a better photothermal performance under 808 nm laser excitation because it has a greater absorbance than probe-1-cRGD at 808 nm, and the results proved that site-isolation principle could play an important role in the optimizing the photothermal performance for the D− π − A type PTAs. Probe-2-cRGD maintained its better photothermal properties in vivo and was found to completely ablate tumors during photothermal therapy. It also demonstrated a distinct photoacoustic imaging signal and enhanced ultrasound imaging signals of tumors in vivo.