The poor storage stability of polymer-modified asphalt (PMA) binder hinders its applications. Traditionally, the softening point test is utilized to evaluate the storage stability, which shows less sensitivity compared with the rheological test. This study attempts to evaluate the effects of polyphosphoric acid (PPA) contents on the storage stability of SBR-modified asphalt binder from empirical, rheological, and molecular aspects. Specifically, the softening point and multiple stress creep recovery (MSCR) test were adopted to assess the phase separation of SBR&PPA-modified asphalt binder. On this basis, the Gel permeation chromatography (GPC) test was used to understand the molecular weight transformation and therefore evaluate the sensitivities of the two tests in revealing the storage stability of PMA. According to the results, 2% PPA is capable to enhance the asphalt binder softening point from 60 ℃ to about 85 ℃. Similarly, the increased PPA contents could also decrease the non-recoverable compliance. When the PPA contents increase from 0% to 2%, the large molecular size proportions climb from 13.5% to about 16%. In addition, PPA with suitable content could enhance the storage stability of the SBR-modified asphalt binder. Yet the softening point difference of asphalt binder containing 1% PPA is merely 0.5 ℃ and reveals the least phase separation according to softening point results, which is contradictory to the best PPA dosage of 0.5% shown in the MSCR and GPC tests. Furthermore, the MSCR test shows better correlations with the GPC test with a correlation coefficient of 0.82. Combining the storage stability and ductility results, the 0.5% PPA content is potential to decrease the phase separation of SBR-modified asphalt binder without substantially weakening the low-temperature performance.