The relationship between the photophysical properties and structure of BODIPY derivatives always has attracted much attention. Two new BODIPY derivative chromophores with phenyl group substitutions at meso-/6- positions, with or without methyl substitutions at 1/3/5/7 positions were investigated by ways of combination of multiple experimental techniques and theoretical methods. The chromophore without methyl substitutions has a larger Stokes shift and better viscosity sensitivity compared to the other one. The intrinsic reason is that considerable charge transfer between the BODIPY core and the 6- position group is achieved in chromophore. However, this charge transfer process is severely weakened, if 1-/3-/5-/7- methyl substitutions existing, via restricting rotation between the core and side groups. At the same time, the non-radiative process is amplified significantly in chromophore without methyl substitution and the fluorescence efficiency decrease from 51.7% (with methyl substitutions) to 1.84% (without methyl substitutions) in DMSO. Quantum calculations indicate the presence or absence of methyl substitution can change both the shape and height of the torsional potential energy curve of the side groups, thereby affecting the fluorescence quantum yield and viscosity response performance of chromophores. Our work can provide foundation and ideas for designing and optimizing BODIPY derivatives with objective photophysical properties.