As an indispensable part of long-distance shield tunnel, the cross passage is usually placed between two tunnels for escape, fire prevention and drainage. Under the action of seismic load, stress concentration is easy to occur at the joint between tunnel and cross passage, which has complex structure and obvious spatial effect, thus resulting in structural damage and immeasurable earthquake damage. Based on the finite difference software FLAC^3D, a three-dimensional model for two-line parallel tunnel and cross passage was established by taking the typical silty clay in Tianjin as an example. Under the input of sine wave, the stress and deformation of the joint between tunnel and cross passage were analyzed, and the effects of tunnel buried depth and the diameter and length of cross passage on the seismic response of joint were discussed. Based on Fish language, a finite difference model which can simulate different incident directions of seismic waves was established. The calculation results showed that different incident directions of seismic waves have a significant impact on the stress of structural joint.