Photothermal agents (PTAs) with ultra-high photothermal conversion efficiency (PCE) activated upon near-infrared (NIR) laser irradiation can heat up and destroy tumor cells under low-intensity laser excitation to allow safe and efficient tumor therapy. Herein, an organic PTA with outstanding PCE of 89.6% is developed from rationally designed perylene diimide (PDI) with electron donating cyclohexylamine moiety at the bay-positions of its skeleton and chiral phenethylamine (PEA) moiety at its N terminals, termed here as PEAPDI. The strong intermolecular interaction between the PDI skeletons induced by PEA together with the intramolecular charge transfer from cyclohexylamine to PDI skeleton severely quenches the fluorescence emission from PEAPDI and significantly enhance its NIR absorption, resulting in super NIR-photothermal conversion. PEAPDI is further encapsulated into silica nanocapsules (SNC) to produce PEAPDI@SNC. The specific features of PEAPDI@SNC, including small hydrodynamic diameter with monodispersity, high PDI encapsulation efficiency, colloidal stability and biocompatibility, effectively extend its blood circulation time and enhance its permeability and retention effect to accumulate at the tumor site. In vivo study using a 4T1-tumor-bearing mice model demonstrates highly effective tumor ablation without side effect at low dosage of PEAPDI@SNC with NIR laser irradiation (808 nm). PEAPDI@SNC shows great potential for photothermal therapy in tumor treatment.