In submerged floating tunnels (SFTs), a next-generation maritime transportation infrastructure, the tunnel module floats in water due to buoyancy. For the effective and economical use of SFTs, connection with the ground is inevitable, but the stability of the shore connection is weak due to stress concentration caused by the displacement difference between the subsea bored tunnel and the SFT. The use of an elastic joint has been proposed as a solution to solve the stability problem, but it changes the dynamic characteristics of the SFT, such as natural frequency and mode shape. In this study, the finite element method (FEM) was used to simulate the elastic joints in shore connections, assuming that the ground is a hard rock without displacement. In addition, a small-scale model test was performed for FEM model validation. A parametric study was conducted on the resonance behavior such as the natural frequency change and velocity, stress, and reaction force distribution change of the SFT system by varying the joint stiffness under loading conditions of various frequencies and directions. The results indicated that the natural frequency of the SFT system increased as the stiffness of the elastic joint increased, and the risk of resonance was the highest in the low-frequency environment. Moreover, stress concentration was observed in both the SFT and the shore connection when resonance occurred in the vertical mode. The results of this study are expected to be utilized in the process of quantitative research such as designing elastic joints to prevent resonance in the future.