Abstract. With regard to increase in growth of population in metropolitan areas around the world, the development of urban infrastructures in a way that is responsive to the population has become a major concern. Today, many cities are willing to use rail transport system which this requires conducting detailed studies of engineers in the field of traffic engineering for the optimal locating in rail lines. Hence in the field of structural and geotechnical engineering for detailed design and structure analysis of tunnels due to applied loads on it and their behavior against the vibrations generated by train movement or earthquake. Then, in order to achieve more realistic results, the urgent need to use three-dimensional analyses and non-linear models can be seen. In the present study, threedimensional analysis of vibrations caused by simultaneous passing of two trains over each other in two tunnels with different directions, three-dimensional analysis of land subsidence caused by excavation of two passing tunnels and three-dimensional seismic analysis of two passing tunnels were discussed with the help of non-linear dynamic modeling. The results of this research showed although the soil at the bottom of the upper tunnel was on the verge of shear failure; however, the relative displacement of tunnels to each other was less than 10 mm. Moreover, the geometry section deformation of tunnels was around 0.8 mm which was negligible values. Thus, the studied tunnels had considerable stability.