To explore the mechanical response of asphalt pavement structure with functional layer, and make asphalt pavement have better service performance, a structural combination form of asphalt pavement with functional layers is proposed in this study, and the interlayer structural mechanical response analysis is carried out based on the theory of a multi-layer flexible layered system. The study first suggests a combined method of stress-strain and displacement at each point of the three-dimensional asphalt pavement structure under the combined compressive-shear load. Secondly, the shear strength of asphalt pavement structure with functional layer under the influence of compressive-shear combined loads, different longitudinal slopes, overload loads, and temperature-elastic modulus under different interlayer contact states are analyzed. Finally, the distribution of structural shear strain of asphalt pavement with a functional layer under different conditions is investigated. The results show that in the asphalt pavement structure with a functional layer, the functional layer is the weak layer of the base-surface layer, and the interlayer shear stress will change abruptly under the combined compression-shear load. The maximum shear stress and extreme strain values are mainly concentrated in the upper and middle surface layers, and they show a consistent trend of first increasing and then decreasing with the increase of the pavement depth. The functional layer can be used as a temperature buffer zone so that the asphalt pavement has good contact performance between the surface and base at 76 ℃ and good shear strength. The results of this study provide a theoretical foundation for studying the interlaminar shear resistance of asphalt pavement with functional layers.