Immersed tunnels, as a form of underwater transportation engineering offering numerous advantages, have been widely deployed in coastal and riverside cities. However, due to the shallow burial and underwater characteristics, immersed tunnels present significantly different surrounding soil and water environments compared to land-based tunnels. Currently, there is limited research on the seismic analysis of submarine immersed tunnels, raising questions about the direct application of the methods of land-based tunnels. In this study, the Davidenkov soil constitutive model is introduced to simulate the strong nonlinearity of deep sedimentary soil in marine areas. The Coupled Acoustic-Structure (CAS) method is employed to simulate the dynamic interaction between seawater and seabed. A time-history analysis model is developed to capture the coupling interactions between seawater, seabed, and tunnel structure. The effects of the soil-tunnel contact mode and seismic input method on the seismic responses of immersed tunnels are investigated in detail. Seismic response characteristics of immersed tunnels are analyzed from four perspectives: distribution of tensile damage in the tunnel, maximum inter-story drift ratio, maximum bending moment, and tunnel inclination angle in the cross-sectional direction. The results indicate that the overlying seawater and sand compaction piles negatively impact the seismic performance of immersed tunnels in the scenarios of this study. Furthermore, their impact pattern and extent are closely correlated with the intensity of the input seismic motion.