Based on the basic equations of linear elastodynamics, combined with the coordinate transformation and Buchwald potential function, the dynamic governing equations for a transversely isotropic multilayered pavement under moving loads are developed. The stiffness matrix for a single layer with a finite thickness and a half-plane are derived by using Fourier transform and its differential properties. Considering the interlayer conditions between layers, the global matrix are assembled with the analytical layer element of each layer. The solutions in the integral transform domain are obtained by combining with the boundary conditions. Then, the corresponding solution in the frequency domain is further recovered by applying inverse Fourier transform. The theoretical derivation of this paper is verified by comparing with the results of the existing literature. The change of interlayer conditions between layers is then simulated by changing parameters. The influence of the interlayer conditions between the surface layer and base layer on the dynamic response of the pavement structure can be calculated and analyzed. The calculation results show that the poor interlayer condition between the adjacent structure layers can cause the poor overall performance and durability of the pavement structure.