Through the establishment of the three-dimensional tunnel-stratum-internal structure model, the effect of different bolt failures on the stress and deformation of the segment structure are analyzed. Furthermore, the sensitivity of the bolt failure to the ground conditions and lining type are discussed. The results show that: (1) The stress-displacement response of the tube segment is elastic under the train vibration load. The position of the vault is not synchronized with the waveforms of other parts. The principal stress fluctuation of the tube segment caused by train vibration is in the arch waist and arch. The bottom is most obvious. The maximum principal stress after superposition appears at the bottom of the arch. The displacement response of the segment occurs mainly in the vertical direction, and the maximum settlement occurs at the bottom of the arch under the influence of train vibration. (2) When single-layer lining is used under the domestic soft soil layer, bolt failure can reduce the stress of the segment, but it will increase the vertical settlement of the segment and the staggered opening of the segment. Considering that the segment stress is far from failure and the steel bars are often designed as over-reinforced, it is recommended to use connecting bolts in soft soil layers. (3) In the soft and hard composite soil layer, the segment stress and the deformation at the joints are reduced to a certain extent. The vertical deformation reduction effect on the segment is significant, and the influence of bolt failure is further weakened. The rationality of not using connecting bolts in shield tunnels with good geological conditions in Nordic and other regions during operation is verified. (4) The use of double-layer lining has little effect on the force of the segment, which can reduce the vertical deformation of the segment to a certain extent, but can greatly reduce the opening and staggering of the joint when the bolt fails. From the perspective of structural safety and stability, a inner lining can be applied to projects with higher safety requirements.