In order to study the effect of vertical seismic on the dynamic response of underground structures, the nonlinear seismic response analysis of a certain metro tunnel in soft sites was carried out. In the numerical analysis, a dynamic nonlinear viscoelastic model was used to model the characteristics of soils under cyclic loading, and the dynamic plastic damaged model of concrete was selected to model the characteristics of tunnel lining. The finite element model was established with dynamic viscoelastic artificial boundary, and the nonlinear seismic response analysis of the model was carried out with the bottom imposed horizontal or two-direction seismic wave. The result shows characteristics of seismic response of the metro tunnel, and that the vertical earthquake wave have a great influence on the relative displacement between tunnel top and tunnel bottom, stress of tunnel and the vertical acceleration at tunnel bottom. Therefore, the effect of vertical earthquake can not be ignored in engineering design.