An experiment involving three neat asphalts and their mixtures with 1.5 wt % of polyphosphoric acid (105%) was conducted to investigate the effect of polyphosphoric acid (PPA) on the long-term aging characteristics of asphalt binders. Analytical techniques including dynamic shear rheometry, Fourier transform infrared (FTIR) spectroscopy, differential scanning calorimetry, and nuclear magnetic resonance (NMR) spectroscopy were performed on unaged and aged PPA-modified asphalts. Rheological properties of unaged and aged modified asphalts were measured with a dynamic shear rheometer at various temperatures. The concentration of carbonyl-containing compounds present in the various unmodified and PPA-modified binders was determined by FTIR spectrometry. The thermal properties of the unmodified and PPA-modified binder were obtained by using differential scanning calorimetry. The results indicate that PPA-modified asphalts reduce rutting potential by increasing initial stiffness and reduce fatigue or low temperature cracking, or both by improving the low-temperature flow properties. The correlation between rheological properties and chemical properties of unmodified and PPA-modified asphalts is also presented. The results show a linear relationship between physical properties and chemical properties of asphalt binders with respect to oxidative aging. However, addition of PPA to asphalt alters the linear relationship. NMR results showed no new chemical species formed in the asphalt-PPA mixture.