Earthquake-induced liquefaction poses a significant threat to underground structures. Particularly, tunnel structures located at the interface of different liquefaction-resistant strata are more prone to severe seismic damages. In this paper, a three-dimensional numerical study was carried out to investigate the seismic response of a shield tunnel passing through saturated sandy strata with different densities. Firstly, a boundary interface model that describes the liquefaction behavior of sand with different densities was used to simulate saturated sand, which was validated by shaking table experiments on a tunnel embedded in liquefiable soil. Secondly, a multi-degree- of-freedom link spring is applied to characterize the interaction between segment rings. The approach was validated using the stepwise loading experimental results of assembled segment rings in Refs. [35] and [37]. Finally, a 3D numerical model of shield tunnels crossing two different densities saturated sand strata was established to study the effects of relative densities of soil, peak input accelerations, and the dip angle of the interface on the dynamic response of sand stratum-tunnel system. The results indicate that horizontal displacements of the tunnel under seismic excitations are coupled with the excess pore pressure induced by vertical uplifts, and deformation of the tunnel is not simultaneous in the two soil strata, resulting in twisting distortion of the tunnel structure. The uplifts of the tunnel change rapidly and are increased with increasing dip angle near the soil interface. Also, bending moments suddenly change, and shearing/tensile displacements of joints increase remarkably, which confirms that the seismic design of underground structure segments near the soil interface is a critical issue.