[Purposes] This paper aims to investigate the differences in compatibility of styrene-butadiene-styrene （SBS） with different molecular structures and block proportions in aged asphalt and waste cooking oil (WCO) mixtures, and to study the influencing mechanism of WCO on the behavior of SBS molecular chains. [Methods] Molecular dynamics was applied to simulate the impact of SBS molecular configuration and block ratio on the compatibility of SBS with WCO and asphalt. The diffusion coefficients of composite reclaimed asphalt molecules were used to evaluate the diffusion capacity of each component, and the solubility, interaction energies and mean square radius of gyration were combined to characterize the compatibilizing effect of WCO on SBS. [Findings] Linear SBS molecules exhibited superior compatibility with aged asphalt compared to star-shaped SBS molecules. A smaller SBS block ratio correlates with increased molecular diffusion capacity, and the reduction of the block ratio promotes the diffusion of SBS molecules into the aged asphalt layer. Linear SBS molecules with a segment ratio of 3∶7 also exhibited the maximum molecular chain size within the system, and WCO has the greatest effect on improving the linear SBS molecules′ compatibility with asphalt. [Conclusions] The molecular configuration and block proportion of SBS significantly influence its compatibility and diffusion behavior in WCO-aged asphalt systems.