In this research, the feasibility of using nano-montmorillonite (MMT) in asphalt binders was investigated in terms of rheological properties, thermomechanical properties, and chemical structure composition. Different doses of MMT were added to the base asphalt and styrene–butadiene–styrene (SBS) asphalt as test subjects. The effect of nanomaterials on the high-temperature resistance of asphalt binders to permanent deformation was analyzed from dynamic mechanical rheology using the multiple stress creep recovery (MSCR) test. The sessile drop method test based on surface free energy (SFE) theory was employed and thermodynamic parameters such as surface free energy, cohesive work, and adhesion work were calculated to analysis the change in energy of the asphalt binder. In addition, changes in the chemical structure and composition of the asphalt binder were examined by Fourier transform infrared (FTIR) and gel permeation chromatography (GPC) tests. The results showed that MMT can effectively enhance the high-temperature elastic recovery and plastic deformation resistance of the asphalt binder. The intercalation structure produced in the asphalt binder enhanced the overall cohesive power and adhesion to the aggregate. The anchoring effect of the intercalation structure resulted in an increase in the macromolecular weight of the binder was demonstrated, indicating that MMT enhanced the overall intermolecular forces of the binder. In addition, the molecular crystal structure was characterized by characteristic functional groups in the infrared spectra, while demonstrating that no chemical reaction occurs during the modification of the binder by the nanomaterials.