In the field of highway construction, the application of styrene–butadiene rubber (SBR)-modified asphalt has gained popularity across different levels of road surfaces. A crucial aspect in ensuring the efficacy of this modification lies in the compatibility between SBR and the matrix asphalt. To address this, the current study utilizes molecular dynamics simulation as a technique. By establishing a model for the SBR-modified asphalt mixture, the research quantifies the compatibility level between the SBR modifier and the asphalt. The aim is to uncover the underlying mechanisms of compatibility between the SBR modifier and the base asphalt, ultimately contributing to the improvement of the storage stability of SBR-modified asphalt, which holds significant importance. The investigation began with the creation of models for both the base asphalt and the SBR modifier. A model for the SBR-modified asphalt blending system was then formulated based on these initial models. After undergoing geometry optimization and annealing procedures, the model attained its lowest energy state, providing a reliable basis for examining the performance of SBR-modified asphalt. The study proceeded to calculate solubility parameters and interaction energies of the system to evaluate the compatibility between the SBR modifier and the base asphalt at various temperatures. The analysis of these parameters shed light on the compatibility mechanism between the two components. Notably, it was found that at a temperature of 160 ℃, the compatibility was significantly enhanced. The findings were further corroborated through scanning electron microscope and rheological tests. The outcomes of this research offer theoretical guidance for the application of SBR-modified asphalt.