Based on the basic control equations of orthotropic anisotropic half-space under moving harmonic loads, the transfer matrix solution of a single-layer foundation is derived by introducing the moving coordinate system, Fourier integral transform, and Cayley-Hamilton theorem. The three-dimensional (3D) dynamic mechanical model of layered orthotropic anisotropic foundation under the rectangular coordinate system is established. The dynamic response of the layered foundation along the depth direction in the frequency domain is derived by using the transfer matrix method, combining boundary conditions, interlayer contact conditions, and continuity conditions. The analytical expressions of the displacements and stresses in the layered foundation are obtained by using Fourier inverse transformation. Based on the derived theoretical method, degradation verification, and corresponding calculation program are prepared for numerical calculation, and numerical example parameter analysis was carried out in combination with the finite element analysis software ABAQUS to study the influence law of the stratification characteristics, load moving speed, load vibration frequency and orthotropic anisotropic properties on the dynamic response of layered foundation. The 3D dynamic characteristics of layered orthotropic anisotropic foundations under the moving load are revealed. The results show that the stratification characteristics of the foundation have a significant effect on the vertical displacement of the surface, and the changes in elastic modulus and shear modulus parameters of the first layer of soil have a greater effect on the displacement dynamic response than that of the subsoil. Within a certain range, the vertical displacement of the foundation surface increases with the increase of load moving speed and decreases with the increase of load vibration frequency. Compared with isotropy, the orthogonal anisotropy of the surface foundation has an obvious influence on the vertical displacement of the foundation surface. In practical engineering, the orthogonal anisotropy of the foundation should be considered in order to obtain more accurate results.