Aiming at the construction requirements under ultra-high temperature conditions, the study systematically reveals the evolution of macroscopic properties of Styrene-Butadiene-Styrene (SBS) modified asphalt during ultra-high temperature aging and its degradation mechanism at the molecular level. The aging process is divided into two stages: heating aging and RTFOT. And four aging temperatures are set in the range of 165–225°C. The effects of different aging conditions on the macroscopic properties of asphalt were analyzed by means of dynamic shear rheometer and bending beam rheometer. The test results show that in the heating aging stage, the complex modulus and rutting factor of SBS asphalt increase first and then decrease with the increase of temperature. After the superposition of RTFOT, both of them turn to monotonically increase. In addition, under the conditions of 205°C and 225°C, the change trend of SBS asphalt phase angle is obviously different from other temperature conditions, showing continuous growth. In terms of low temperature performance, the stiffness modulus of SBS asphalt increases first and then decreases with the increase of heating aging temperature, while the creep rate shows a U-shaped change. After RTFOT, both of them show a one-way evolution trend. In order to explain the degradation mechanism from the perspective of SBS cracking behavior and molecular structure of modified asphalt, this study further combined fluorescence microscopy and nuclear magnetic resonance techniques for analysis. The results show that when the aging temperature exceeds 205°C, the SBS molecular chain undergoes significant cracking and agglomeration. And the aromaticity and the decay rate of H_β+H_γ are significantly accelerated. Based on the improved Brown-Ladner model and gray relational analysis, it is proposed that the I_C=O and the f_A1 can be used as the key evaluation indexes for the degradation of ultra-high temperature performance.