To explore the effect of compatibilizer composition on the anti-aging properties and microstructure of SBS modified asphalt, the compatibilizers with different compositions were prepared for SBS modified asphalt samples, and the changes in performance and microphase before and after aging were evaluated by conventional performance test, dynamic shear rheology test and fluorescence microscopy. The results show that the higher the aromatic content in the compatibilizer is, the better the high temperature properties of SBS modified asphalt are, while the higher the saturate content is, the better the low temperature performance of the modified asphalt are. After aging, the higher the aromatic content in the compatibilizer is, the smaller the variability in the various properties of the modified asphalt is, that is the better anti-aging properties; Conversely, the higher the saturated content is, the worse the anti-aging properties are. Meanwhile, the microstructure shows a distinct aggregation phenomenon. The higher the saturate content is, the more severe the aggregation and the larger the particle size are. The system changes from double continuous phase structure to the SBS phase as the dispersed phase and the asphalt phase as the continuous phase structure.