Abstract: To address the challenge of seismic input for the “seawater-seabed-bedrock” multiphase medium system in complex marine engineering sites, this paper establishes an efficient theoretical framework and numerical simulation method for seismic input applicable to multi-layer marine sites. Based on wave theory, an analytical solution for the free-field response of a half-space site containing an overlying seawater layer under oblique SV wave incidence is derived, revealing the propagation, reflection, transmission, and waveform transformation patterns of seismic waves at the interfaces of the multiphase medium. By introducing artificial boundary conditions for fluid and solid media to achieve high-precision truncation of the infinite domain, and by combining the artificial boundary substructure method to convert the free-field response into equivalent node forces, the method successfully achieves precise input of obliquely incident seismic motion into the “seawater-seabed-bedrock” coupled system. Using single-pulse and typical seismic wave scenarios, comparative validation of the evolution of the multi-medium wavefield under different incidence angles was conducted. The results indicate that the numerical solutions for displacement responses at monitoring points in each medium layer are highly consistent with theoretical analytical solutions in terms of amplitude, phase, and waveform characteristics, with the maximum relative error strictly controlled within 4%. The method proposed in this paper provides theoretical support and an efficient analytical tool for assessing the seismic resilience and safety design of major marine infrastructure, such as coastal nuclear power plants.