Abstract: In the actual foundation-tunnel system, the properties of soil and structures often change longitudinally along the tunnel line. In order to consider the longitudinal variation characteristics of structures, a multi coupling periodic finite element method for dynamic response analysis of unsaturated soil-structure system is proposed in this paper. Firstly, based on the practical wave equation of unsaturated soil, the finite element expression of u_b-p_l -p_g scheme for unsaturated soil with 5 degrees of freedom at a single node is derived by Galerkin method, which can save the computing efficiency compared with the finite element expression of u_b-v-w scheme with 9 degrees of freedom at a single node. Then, by introducing the stretching function with complex number, the perfectly matched layer boundary element is constructed to truncate the infinite domain. Finally, multi periodicity is used to simulate the longitudinal variation characteristics of the structure. By introducing the free wave propagation theory and combining the continuity conditions between periodic structures, the coupling between periodic structures can be realized. The results of the proposed method are compared with the results obtained by the existing 2.5 dimensional coupled FE-PML model and analytical method respectively, which verified the reliability of the proposed method. Compared with the existing analytical methods or numerical methods, the proposed method has the advantage of considering the longitudinal variation characteristics of the structure efficiently. Based on the proposed method, taking unsaturated soil-tunnel-isolation pile system as an example, the vibration reduction and isolation effect of isolation pile is discussed. The results show that compared with gnawing piles, the regular of surface dynamic response changes after considering the spacing between isolated piles. Therefore, in order to accurately predict the vibration response of subway tunnel system, the longitudinal variation characteristics of the system structure should be taken into consideration.