Based on the discrete element method (DEM), this study conducted the virtual simulation of wheel tracking tests to predict the rutting deformation of asphalt mixtures and analyzed the micromechanical response of aggregate skeletons within the asphalt mixture during the tests. Considering the irregular shape and elastic property of coarse aggregates, the continuum and viscoelastic property of the asphalt mastic and the random distribution of air voids in the asphalt mixture, a three-dimensional micromechanical DEM model for asphalt mixture was constructed by particle flow code in three dimensions (PFC3D). A two-dimensional virtual asphalt mixture sample was generated based on the central cross-section of the three-dimensional virtual asphalt mixture sample. A virtual wheel tracking test was built by PFC3D and verified by laboratory wheel tracking tests to predict the rutting behavior of the asphalt mixture. During the virtual wheel tracking test, the movements of the coarse aggregates, including their translation and rotation, were revealed, and the contact condition and contact forces within the aggregate skeleton were analyzed. The micromechanical responses of the aggregate skeleton demonstrate how the aggregate skeleton in asphalt mixtures bears the load and describes the potential reasons why rutting deformation forms from the micromechanical view.