It is a challenge to develop multifunctional theranostic agents in one molecule, which simultaneously possesses tumor imaging ability with a high signal-to-noise ratio and excellent therapeutic activity. In this work, we synthesized and screened a series of BODIPY (BDP) with various absorption and fluorescence. The interplay of the molecular structure, pH-sensitive absorption and emission, and photodynamic and photothermal activities was well studied in detail. Photoinduced electron transfer, intramolecular charge transfer, and heavy atom effect were leveraged to engineer BDP with tumor imaging and therapeutic functions. The BDP nanoparticle formulations possessed multifunctional biological features, including selective treatment of cancer cells, near-infrared fluorescence, photoacoustic and computed tomography imaging, and photodynamic and photothermal therapy, as validated by cellular and animal experiments. These results not only give a new horizon to multifunctional BDP for biological applications but also show a new way to design the organic dye for tumor imaging and phototherapy.