The selection of accurate input design parameters is important for understanding the dynamic response of an asphalt pavement structure. The transverse and longitudinal shear stresses that affect the dynamic response of asphalt pavement are not considered in traditional asphalt pavement design. To this end, this study utilizes the finite element method (FEM) to analyze the mechanical response of asphalt pavement under dynamic loads with non-uniform tire-pavement contact stresses. For this purpose, firstly a three-dimensional (3D) finite element (FE) model of a rubber tire is developed. Secondly, the predicted and laboratory measured stresses are compared to develop a 3D FE model of the contact stresses. Finally, a 3D FE model of the tire–pavement contact is analyzed to investigate the influence of shear stresses on the response of the asphalt pavement and the superposition effect of the mechanical response. The results show that the distribution and magnitude of the vertical contact pressure under the free-rolling state are the same as those under the static state, and the traction and braking conditions could change the symmetry of tire-pavement interactions. In addition, the shear stress at the tire-pavement interface affects the peak response of the surface layer, indicating that shear stress plays a considerable role in controlling the development of rutting and longitudinal cracks. Considering the viscoelasticity of the asphalt material, it is observed that the superposition effect of the mechanical response is a comprehensive result of the space–time domains. In conclusion, this study analyzes the influence of tire-pavement contact on the mechanical response of asphalt pavement and proposes input design parameters for improving the design of asphalt pavement.