Based on the structural viscoelastic boundary theory, considering the geological changes of the soil layer and depth of tunnel crossing, the dynamic time course analysis is carried out for the defective lined tube sheet structure under non-uniform seismic excitation, to obtain the force and deformation law of the whole tunnel structure as well as the defective section. Analyze the dynamic response of shield tunnel structure under non-consistent seismic excitation under the influence of tube sheet misalignment factors, summarize the intrinsic mechanism of the dynamic response of defective tunnel tube lining structure, identify the phenomena affecting lining junction damage, and refine the seismic safety evaluation method of defective lining structure.