BODIPY dyes have some unique properties including high fluorescence quantum yield, large extinction coefficiency, narrow absorption and emission band. However, most of BODIPY dyes display short emission wavelength and small Stokes shift, which limits their applications in biosensing and bioimaging in vivo. For bioimaging application, a fluorescent dye with long emission wavelength and large Stokes shift is highly desired. To push the absorption and emission spectrum of BODIPY to red and even far-red region, a COOEt group was introduced to the meso position, and some aromatic group was attached to the 3,5 position of BODIPY core. The structure of resulting compounds were comfirmed by 1H NMR, 13C NMR and HR-MS. Dye-1 displays a strong UV-Vis absorption band centered at 536 nm and a sharp emission band is located at 592 nm, which is significantly red-shifted (80 nm) compared to ordinary BODIPY analogs. In addition, the meso-COOEt substituted BODIPYs exhibit high quantum yield and red to far-red emission. Notably surprisingly, the meso-COOEt substituted BODIPYs display almost separated UV-Vis absorption and emission spectra with a large Stokes shift (~60 nm). Time-dependent density functional theory calculations were conducted to understand the structure-optical properties relationship, and it was revealed that the large Stokes shift was resulted from the geometric change from the ground state to the first excited singlet state. The spectroscopic properties of these BODIPY dyes display very subtle solvent-dependence effect. Furthermore, BODIPY was tested for its ability of imaging in living cells. The results indicate that Dye-1 is a water-soluble and membrane-permeable probe. Therefore, these BODIPYs are a new family dyes with excellent spectroscopic properties and can be good candidates for bioimaging in living cells.