Fluorescence microscopy technology was conducted to characterize the microscopic morphology of SBS modifier in asphalt binder, and the effect law of different SBS content, shear temperature and shear rate during the modification, on the microscopic morphology of SBS modifier is discussed. SBS area ratio, box dimension, area-weighted average axis ratio, coefficient of variation in axis ratio, average particle area and coefficient of variation in particle area were defined to characterize the SBS morphologies. Relation between SBS microscopic morphology and the viscoelastic properties of asphalt binder was also established. Results show that the area ratio of SBS particle has linear relationship with the SBS content, while higher SBS content has negative impact on the SBS distribution in asphalt binder. Increasing shear temperature can reduce the size of SBS particles from 7 to 10 μm at 130 °C to 4–5 μm at 175 °C. Higher shear rate brings stronger mechanical effect to SBS asphalt, which makes the physical dispersion of SBS more uniform, the specific surface area of fine particle size is larger, and the area ratio increases due to sufficient swelling effect. The rutting factor of SBS asphalt is greatly affected by the microstructure of SBS modifier. The modified Einstein model and modified Maron and Pierce and Quemada model can be successfully used to describe the relation between rutting factor of asphalt binder and morphologies of SBS modifier in the binder. This study provided a good technic to enhance the quality of SBS modified binder and its corresponding mixture by means of improving the SBS morphologies in asphalt binder.