Subway tunnels crossing soft ground under seismic action are susceptible to severe damage. Therefore, the study of seismic response and damage characteristics of tunnels under this type of stratum is essential for the safe operation of subways. To this end, the elastic-plastic equations reflecting the concrete damage are first derived by combining the segmental curve damage model and the Druker-Prager elastic-plastic model. Then, a soil-shield tunnel interaction model based on the damage model of concrete pipe slice is established with the help of FLAC3D finite difference program and secondary development interface. Finally, the dynamic response and structural damage of shield tunnels under the influence of seismic waves in horizontal and vertical directions are investigated. The results show that: (1) The uniaxial tensile and compressive tests with FLAC3D software show that the elastic-plastic damage model can reflect the mechanical damage characteristics of concrete and the softening development of the material, thus verifying the reasonableness and accuracy of the model. (2) The dynamic response and damage degree of the shield tunnel show positive correlation with the seismic amplitude. The maximum damage increment locations of the tunnel structure under the action of horizontal direction seismic waves and vertical direction seismic waves are at the foot of the tunnel arch, at the shoulder of the arch and at the sides of the tunnel, respectively. Among them, the effect of the incident seismic wave in vertical direction on the damage degree of the tunnel is more significant.