Based on the small-amplitude water wave theory, an analytical investigation is performed for the interaction between incident waves and a multi-modular very large floating structure (VLFS) in a two-layer fluid with a flexible seabed. A vertical porous flexible plate is fixed in the center of each floating plate to suppress the hydroelastic response. A key innovation is the modeling of both the VLFSs and the seabed as thin elastic plates with the lateral stress. The analytical expressions for dispersion relationships and vertical eigenfunctions are exactly derived in the water regions with a flexible seabed. The series solution of the velocity potential is obtained through the combination of inner product and the least squares approximation method. The study uniquely illustrates the impact of lateral stress and flexible seabeds on wave propagation, revealing that at low frequencies, waves in both open water and plate-covered regions with a flexible seabed exhibit the similar propagation characteristics. At higher frequencies, however, the propagation characteristics of the waves in the open water regions remain unaffected by the presence of a flexible seabed. The lateral stress has significant effects on the roots of dispersion relationships and the hydroelastic responses. The influences of other physical parameters of the fluid and structures are also displayed graphically. The results demonstrate that the increasing number of modules and extending the vertical plates effectively suppress hydroelastic responses and reduce wave transmission. The porous barriers can reduce the stress on the vertical plates and weaken the effect of barriers for suppressing hydroelastic response.