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Interfacing and compatibility are the most challenging issues that affect the performance of polymer modified asphalt. Mechanisms of interfacial enhancement among four base asphalt components (asphaltenes, resins, aromatics, and saturate), styrene-butadiene-styrene (SBS), and carbon nanotubes (CNTs) were investigated by molecular dynamics simulation, with the aim of understanding the key parameters that control the compatibility of CNTs and interphase behavior on the molecular scale. The compatibility of SBS-modified asphalt (SBSMA) was simulated based on self-assembly theory using indexes of binding energy, mean square displacement, diffusion coefficient, and relative concentration distribution. The interphase behavior and microstructure were observed by fluorescence microscopy and scanning electron microscopy. In addition, a rutting experiment was used to verify the molecular dynamics simulation based on macroscopic performance. The results showed that after adding CNTs, the binding energy of the SBS and aromatics increased from 301.8343 to 327.1102 kcal/mol. The diffusion coefficient of the SBS and asphaltenes decreased more than 3.2×10?11 m2/s, and the correlation coefficients between the diffusion coefficient and the molecular weight, surface area and volume were all lower than 0.3. Relative concentration distribution curves indicated that CNTs promote the ability of SBS to swell. Microscopic observations demonstrated that the swelling ability of SBS was increased by CNTs. Overall, the interphase of SBSMA was improved by the additional reinforcement, swelling, and diffusion provided by CNTs. Finally, the rutting experiment found that no matter what the temperature, the rutting factor of CNT/SBSMA is higher than that of SBSMA, which corroborates the findings from the molecular dynamics simulations.