Despite the merits of using polyphosphoric acid (PPA) in modification of bitumen, its desirable stiffening effect on bitumen is totally composition-dependent. While asphaltenes and resins are correctly introduced as the immediate components affected by PPA, our laboratory rheological investigations show that bitumen's wax content could be a potential interference for PPA's modification function. As evidenced by the complex viscosity test, PPA is very effective in low-wax bitumen, but its effect on high-wax bitumen is quite negligible. In a high-wax medium, the trend of interaction energy improvement with the number of wax chains suggests that the crystalline networks of wax can interfere in interactions of PPA with either asphaltene or resin through concealing interaction sites of asphaltene and resin. This in turn leads to the reduction of their accessible active sites for interacting with PPA. To study the working mechanism of PPA on bitumen constituents, the density functional theory (DFT) approach and energy decomposition analysis (EDA) were performed on the pairs of PPA−asphaltene, PPA−resin, and PPA−wax molecules. In the case of the PPA−asphaltene interaction, EDA shows clear contributions of electrostatic, orbital, and dispersion forces. In the resin fraction, the strong interactions between basic sites of the resin molecules and PPA lead to the formation of ion-pair compounds stabilized through oppositely charged ions held together via Coulombic attraction. The formation of these new entities, which are often nonsoluble in heptane, can further explain the decrease of resin content after PPA modification. The reduction of resin is followed by an increase in the content of asphaltene with a smaller molecular weight in n-heptane precipitates, which is in line with our experiments and that of other researchers.