Abstract: During the construction of utility tunnels, it is inevitable to pass through non-homogeneous soil, leading to adverse effects on the seismic resistance of tunnels. The dynamic deformation response and interaction between the non-homogeneous soil and the utility tunnel under seismic action were systematically studied through a shaking table test. The results of earth pressure increment, acceleration, displacement, and strain were analyzed, including the vertical distribution of the acceleration peak values and the response laws of the direct influencing factors of the tunnel deformation. It is found that the amplification effect of acceleration is attenuated due to the existence of underground structures; the slippage between soil and tunnel occurs during large earthquake, which has a great influence on the deformation of the tunnel; with the increase of acceleration, the distribution of earth pressure increment is approximately parabolic; a larger flexibility ratio of a structure leads to a larger deformation. Based on the shaking table test results, the simplified calculation method of the tunnel through the non-homogeneous soil was studied, and the influence of the soil boundary on the deformation of the tunnel is realized by adjusting the racking ratio, which provides a reference for the seismic design of utility tunnels.