Pushing forward the red-shifting of electronic transitions in organic dyes is potentially important for applications in photodynamical chemistry and therapies. In this work, a series of BODIPY derivatives conjugated with azulene at different substituent positions were synthesized and investigated in depth. These compounds are shown to exhibit varying bathochromic shifts of their electronic transitions, as well as a further red-shift of the absorption by the modification of the compounds with iodine. Moreover, self-assembly and protonation of these compounds lead to hundreds of nanometer red-shifted electronic transitions, up to NIR-II window, relative to traditional BODIPYs. On this basis, a unique photoproduction of singlet oxygen species can be achieved under corresponding long-wavelength irradiation both in organic solution and in water, featuring a superior photosensitivity and photodynamic potential of the molecular design.