The aim of this research is to evaluate the effect of polyphosphoric acid (PPA) on the mechanical performance of styrene–butadiene–styrene (SBS) and styrene–butadiene–rubber (SBR) modified asphalt. Conventional properties, multiple stress creep recovery (MSCR), bending beam rheometer (BBR), and linear amplitude sweep (LAS) tests were conducted to evaluate the performance characteristics of asphalt at different PPA inclusions. Gel‐permeation chromatography (GPC), saturates, aromatics, resins, and asphaltenes (SARA), and Fourier transform infrared (FTIR) were carried to reveal the molecular weight, component and infrared spectra of asphalt. Results showed that PPA hardened the asphalt, improved the rutting and fatigue performances of polymer modified asphalt (PMA) binder, but weakened the anti‐cracking performances. Besides, storage stability had a significant improvement as the addition of PPA. The addition of PPA brought more macromolecules into asphalt and led to more high‐average molecular weight compounds. Furthermore, PPA changed four component ratios of asphalt. Both PMA with or without PPA have similar absorption peaks. This may be due to absorption peak of PMA covered the changes in PPA modification process as the low content of PPA. 0.8% dosage of PPA may be considered optimum for composite modified binder combining the above experimental results for this binder source.