Abstract: In order to study the effect of natural soil structure on tunnel construction and the influence of water-soil coupling of finite element calculation, based on the elasto-plastic model, the soils with different initial structures are chosen, to analyze the interaction between the tunnel and the soils. The finite element analysis results show that in the saturated soft soil layer, after excavation, with gradual decrease of pore pressure, the structure of the soils surrounding the tunnel slowly disappears, the long-term deformation of soil strata is caused, and the stress of the adjacent pile foundation also needs long time to be stabilized. The larger the structured soils, the greater the surface subsidence and the larger bending moment of the adjacent piles will be caused.