The polyphosphoric acid (PPA) modified asphalt binder is a potential choice as one of the pavement materials for its excellent high-temperature performance and low cost. To further analyze the influences of temperature and load on the service life of pavement from the perspective of deformation behavior, six kinds of asphalt binders with different PPA dosages were prepared for Multiple Stress Creep and Recovery (MSCR) tests at five temperature levels. The deformation behavior is investigated by basic deformation parameters, rheological simulation, and energy parameter changes. The results show that the percent recovery (R) drops sharply while non-recoverable creep compliance (Jnr) goes up slightly with the increase in temperature. Three-element model, composed by E1, η1, and η2, can be used to describe the creep behavior. PPA-modified asphalt binder exhibits nonlinear creep behavior, and the logarithmic model can simulate recovery behavior better than the power–law model. Stored energy and dissipated energy can characterize the change of energy in the creep process under different conditions and show a significant correlation to deformation parameters. It is concluded that the elastic component of asphalt binders is increased by PPA, which is beneficial to the improvement of the deformation resistance and recovery capacity of asphalt binders. The recommended dosage of PPA is 1.5%. This investigation is conducive to a better understanding of the deformation behavior of PPA-modified asphalt binders and provides a reference for its engineering applications.