The ultraviolet (UV) aging of asphalt is an important factor affecting the long-term performance of asphalt pavement, especially in high altitude cold regions. The current studies have reported that styrene butadiene rubber-modified asphalt (SBRMA) has a good cracking resistance at low temperatures. In addition, polyphosphoric acid (PPA) is an effective modifier that can enhance the anti-UV aging properties of asphalt. However, the understanding of the improvement mechanism of PPA on the anti-aging of SBRMA remains unclear. Therefore, this study aimed to evaluate the effect of PPA on the UV aging resistance of SBRMA. The rheological properties of PEN90 asphalt(90#A), SBRMA, and PPA/SBR modified (PPA/SBR-MA) before and after UV aging were evaluated by dynamic shear rheometer (DSR) and bending beam rheometer (BBR) tests. The molecular weight and chemical structure of 90#A, SBRMA, and PPA/SBR-MA were determined by Fourier transform infrared spectroscopy (FTIR) and gel permeation chromatography (GPC), and the interaction and modification mechanism of the modifiers were analyzed. The rheological analysis shows that the high and low temperature performances of SBRMA are improved by adding PPA, and PPA also significantly reduces the sensitivity of SBRMA to UV aging. The microscopic test results show that PPA has a complex chemical reaction with SBRMA, which results in changes in its molecular structure. This condition enhances SBRMA with a more stable dispersion system, inhibits the degradation of the polymer macromolecules of the SBR modifier, and slows down the aging process of base asphalt. In general, PPA can significantly improve the anti-UV aging performance of SBRMA. The Pearson correlations between the aging indexes of the macro and micro properties are also significant. In summary, PPA/SBRMA material is more suitable for high altitude cold regions than SBRMA, which provides a reference for selecting and designing asphalt pavement materials in high altitude cold regions.