In complex environments, tunnels with a lined structure are more affected by the dislocation of a segment. This study uses finite element simulations to further investigate the relationship between environmental changes and segments in lined tunnels. Tunnels with and without a lining are simulated under varying strata resistance, buried depth, and water level conditions. The horizontal and vertical displacements and stress changes in the two tunnels are compared when segment dislocation occurs. The results show that the lateral displacement of the tunnel is relatively stable and less influenced by external loads. However, the longitudinal displacement change is the opposite, and it increases significantly when the displacement exceeds 10 mm. When the lined tunnel is subjected to a large external load and misalignment occurs, the performance of the tube sheet joint bolts deteriorates, resulting in a stress decrease. Furthermore, the lined tunnel exhibits an increased ability to resist deformation and does not exactly follow the law of small displacements from small misalignments. When a large misalignment occurs, the lined tunnel may be damaged by elliptical deformation along the 45° direction, and its internal forces would be much larger than those of the unlined tunnel.