With the construction of Super long tunnel , different structural strata as well as some weak interlayers and faults inevitably pass through. The soft interlayer itself is a kind of weak geological structure with loose structure, weak mechanical properties and strong variability between different layers. In the process of tunnel construction, excavation disturbance causes stress redistribution to the original rock, which makes the weak interlayer in unstable, which has potential threat to the safety of tunnel construction. Therefore, by using the method of three-dimensional numerical analysis ，tunnel excavation disturbance across the weak intercalated structure stress distribution and deformation law of different parts are analyzed。Based on the characteristics of stress and displacement distribution，targeted support measures are put forward for the tunnel construction process, and provides a reference value for the study of the stability of tunnel excavation.