The reasonable structure of aza-BODIPY renders it as an efficient photothermal reagent for photothermal therapy. Herein, we describe the design and synthesis of aza-BODIPY NMeBu with the free rotating tert-butyl group and the dimethylamino-substituted segment to promote the photothermal conversion via the excited state non-radiative transition. NMeBu was found to be the π-π stacking form in the unit cell based on X-ray analysis. NMeBu-NPs by self-assembly possessed a near-infrared absorption (λabs = 772 nm), and once activated by near-infrared light, the photothermal efficiency in aqueous solution can reach 49.3%. NMeBu-NPs can penetrate the cell and trigger cell death via the apoptosis pathway under low concentration and low light power irradiation, thereby avoiding dark toxicity. Aza-BODIPY created using this procedure has excellent photothermal efficiency and could serve as a potential candidate for the treatment of cancer cells and tumors.