Understanding the modification mechanism of C9 petroleum resin (C9PR) on styrene–butadiene–styrene (SBS) polymer modified asphalt properties is of significant importance. In this paper, dynamic shear rheometer (DSR), storage stability, fluorescence morphology (FM), scanning electron microscope (SEM), Fourier transform-infrared (FTIR) spectrometer, and molecular dynamic (MD) simulation were adopted to evaluate the rheological, chemical, and microstructure molecular motion state of C9PR and SBS composite modified asphalt at different aging states. The DSR storage results indicate that the addition of C9PR could improve the high-temperature property, storage stability, and temperature susceptibility. FM and SEM results indicate that the network microstructure was enhanced and the roughness between polymer resins and virgin asphalt was improved at the microscopic scale. The MD results indicate that the heterogeneity between C9PR and SBS modified asphalt was demonstrated, and the bonding energies were enhanced with the addition of C9PR. Moreover, the FTIR results indicate that new function groups were generated in addition to C9PR. In general, the addition of C9PR is a good approach to promote high-quality polymer modified asphalt (PMA) for pavement engineering.