Asphalt migration is one of the significant detrimental effects on asphalt pavement performance. In order to simulate the state after the occurrence of asphalt migration amid asphalt pavement layers and further investigate the effects of asphalt migration on the dynamic modulus of asphalt mixture, samples with different asphalt contents layers were firstly separated into the upper and lower half portions and then compacted together. By conducting the dynamic modulus test with the Superpave Simple Performance Tester (SPT), the variation laws of the dynamic modulus (|E*|) and the phase angle (δ) at different testing temperatures and loading frequencies were analyzed in this paper. Further, the dynamic modulus and the stiffness parameter (|E*|/sinδ) at the loading frequency of 10 Hz and testing temperature of 50 °C were illustrated. Simultaneously, the master curves of the dynamic modulus and phase angle of asphalt mixtures under different testing conditions were constructed to better investigate the effects of asphalt migration on the dynamic modulus by means of Williams–Landel–Ferry (WLF) equation and Sigmoidal function. Results show that, after the asphalt migration, the dynamic modulus of asphalt mixtures increase with the increasing loading frequency while they decrease with the increasing testing temperature; the dynamic modulus and the stiffness parameter are the highest when asphalt mixtures have the optimum asphalt content layers, and then decrease with the incremental difference of asphalt content in the upper and lower half portions. Besides this, different from the master curves of dynamic modulus, the master curves of phase angle firstly increase with the increase of loading frequency to the highest point and then decrease with the further increase of loading frequency and are not as smooth as that of dynamic modulus. It can be concluded that the asphalt migration has compromised the mixture’s mechanical structure, and the more asphalt migrates, the weaker the mechanical properties of asphalt mixture will be. Additionally, based on the shift factors and master curves in the time–temperature superposition principle (TTSP), the effects of asphalt migration on the dynamic modulus and the variation laws of the dynamic modulus of asphalt mixture after the occurrence of asphalt migration can be better construed at the quantitative level.