In this article, a frequency domain modal decomposition method is proposed to determine the hydrodynamic response of a submerged floating tunnel subjected to wave forces. In this method, using the 3D finite element method (FEM) to solve the modal functions and 2D high-order matched boundary element method (HOBEM) is used to solve the hydrodynamic problem of the structure. Using modal decomposition method, the modal functions of the structure are Fourier expanded and combined with 2D hydrodynamic coefficients to construct the 3D generalized hydrodynamic coefficients and generalized wave excitation forces. Among them, the generalized wave exciting force is calculated by considering the ratio of the tunnel’s cross-sectional area to the incident wavelength, using either the Morison equation or the potential flow theory. During the research process, the influence of key structural parameters, such as cables diameter and pipe length, on the inherent properties of the system was examined. Additionally, the research compared the effects of various methods for calculating the added mass on SFT displacement. Finally, the research presented that how wave frequencies and incident angles affect the structural dynamic response under wave actions.