Compatibilizers play a critical role in resolving compatibility issues between styrene–butadiene–styrene (SBS) modifiers and asphalt systems. These additives enhance the uniform dispersion of SBS modifiers and stabilize their cross-linked network structure within the asphalt matrix. This study employed molecular dynamics (MD) simulations via Materials Studio (MS) to investigate the effects of a compatibilizer on compatibility mechanisms and diffusion behavior in SBS-modified asphalt (SBSMA). Model validation was conducted through density and glass transition temperature (Tg) analyses. The cohesive energy density (CED) and solubility parameters were quantified to assess the impact of compatibilizer dosage on system compatibility. Radial distribution function (RDF) and mean square displacement (MSD) analyses elucidated molecular diffusion dynamics. The results indicate that compatibilizers enhance cohesive energy density by 12.5%, suppress irregular intermolecular motion, and reduce system instability. The synergistic interaction between aromatic and saturated components in compatibilizers effectively disperses asphaltene aggregates and inhibits π–π stacking. Additionally, strong solubility interactions with hydrocarbon mixtures facilitate the diffusion of asphaltene gum molecules. These findings provide molecular-level insights for optimizing compatibilizer design in SBSMA applications.