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This paper is concerned with the dynamic interaction between soil, pile and structure when subjected to harmonic excitation at the base rock level. The structure to be analysed is an isolated tall bridge pier with deep group pile foundation. The dynamic substructure approach is taken, dealing first with the pile‐footing substructure and the pier superstructure independently; and then integrating these at the interface. Since the soil profile is multi‐layered, the transfer matrix scheme is applied to extend the relevant continuum solution proposed by earlier researchers for pile analysis in a homogeneous viscoelastic medium. Using a numerical example, the importance of the soil layer vibration modes which exert forces on the pile varying along the pile length is pointed out together with the soil‐structure inertial interaction in the structural response. The latter concerns the dynamic characteristic of the complete system whereas the former relates the driving force to it. Also examined is the applicability of the approximate soil reaction based on the plane strain assumption, which simplifies the formulation and requires much less computing time in the response analysis.

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