This paper concerns the impact of an operating metro train on the structure of a shield tunnel lining and its soft foundation. An elastoplastic 3D dynamic finite difference model was established by using the FLAC3D numerical software. By fully considering the joints, the A-B-K segments and the soft stratum, the dynamic response of the shield tunnel buried in thick, soft soil under the vibrating load induced by a metro train was numerically simulated. The simulation result, for which the joint was considered, was compared with the result when the joint was not considered. The results show that an operating metro train induces a significant dynamic response in the structure of the lining of the shield tunnel and its soft foundation. The severe dynamic response zones of the lining structure are largely distributed in the range of the lower half of the segment-ring and the nearer to the bottom of the segment-ring, the more severe the response. Of two horizontally symmetric, corresponding places on the segment lining, the one near the joint is more severe in its dynamic response than that of the one far from the joint; the nearer the zone of the foundation soil to the lower half of the segment-ring, the more severe the dynamic response. The maximum shear strain of the foundation soil takes place near the joint between two normal segments at the bottom. The dynamic response influenced by joints is more severe than the response not influenced by joints, showing that the non-joint assumption is somewhat impractical.