The segment misalignment is a common defect in the segment installation of a shield tunnel construction, due to the complexity and uncertainty of its construction conditions. This raises a concerning about the safety of the segment lining for the shield tunnel. In this paper, the integrated numerical models with surrounding rock, peastone grouting and segment lining were built using three-dimensional finite element method, by introducing two kinds of misaligned defects of segments. One was the misalignment that elongated the horizontal axis of the transversal ring section of segment lining, another was the misalignment between adjacent rings of segments. To eliminate the impact of boundary on numerical results, seven rings of segments are built for the three-dimensional finite element models, and the middle ring is dealt with for the results analysis under V-class surrounding rock, including the circumferential stress of outer and inner layers of the segment, the contact stress on joint surface between segments, and the stress of locating pins between adjacent rings. Results indicate that the two kinds of misaligned defects create pronounced impact on tensile stress of segment at the bottom and the crown segments, respectively, which produces a greater tensile stress to increase cracking risk even abrupt fracture of segment. However, the misaligned defects have a slight impact on the contact stress and the locating pins stress. Therefore, attention should be paid to the cracking of bottom or crown segments in the segment lining of shield tunnel.