The interfacial characteristics between asphalt and aggregates significantly influence the performance of asphalt mixtures. However, conventional experimental approaches based on phenomenological theory fail to adequately characterize these interfacial properties due to their scale features. In order to deeply explore the interfacial properties of rock asphalt/styrene-butadiene rubber composite modified asphalt-aggregates, the molecular models of virgin asphalt, RAMA (rock asphalt modified asphalt), SBRMA (styrene butadiene rubber modified asphalt) and RSMA (rock asphalt/styrene butadiene rubber composite modified asphalt) were first established in this study. On this basis, the asphalt-aggregate interface molecular models were constructed. Through molecular dynamics simulation, the diffusion characteristics, aggregation characteristics and adhesion properties of different asphalt-aggregate interfaces were analyzed. In addition, the pull-out tests of asphalt-aggregate were carried out to verify the simulation results. The results show that the light components in the virgin asphalt have better fluidity than the polar components. The polarity of SBR molecules is weaker than that of RA molecules, but both will inhibit the movement of asphalt molecules. After the composite modification of RA and SBR, the inhibitory effect on the mobility of asphalt will be superimposed. Asphaltene and RA molecules have stronger molecular polarity, so they are more likely to aggregate on the surface of aggregates than other components. The polarity of SBR molecules is relatively weak and will only affect the aggregation characteristics of light components. The increase in temperature will reduce the adhesion work of asphalt-aggregate. When the temperature remains unchanged, the adhesion work from large to small is RAMA > RSMA > SBRMA > virgin asphalt. The simulation results of the adhesion of work are in the same trend as the pull-out test results, indicating that the research has a certain rationality.