The regulation of photochemical properties of phototheranostics, especially the absorption, fluorescence, singlet oxygen (1O2) generation, and photothermal conversion efficiency, is a hot research topic. Here, we designed and synthesized four boron dipyrromethene (BODIPY) derivatives with high absorption coefficients and intense fluorescence in the near-infrared (NIR) region. The substituted electron-donating group significantly improved 1O2 generation and fluorescence of BODIPYs, whereas the electron-withdrawing group boosts photothermal conversion. These hydrophobic BODIPYs were further coated with DSPE-PEG-2000 to form water dispersible nanoparticles (NPs). Among these BODIPY NPs, the B-OMe-NPs with methoxyl substituted at the meso-position showed the highest 1O2 generation, a photothermal conversion efficiency of 66.5%, and an NIR fluorescence peak at 809 nm. In vitro and in vivo experiments demonstrated that B-OMe-NPs might be used for NIR fluorescent and photoacoustic imaging-guided photodynamic and photothermal therapy of cancer.