This study presents the fatigue performance of the mooring lines for submerged floating tunnels (SFTs), the new type transportation system for land connection. Because of the structural characteristics, the submerged structure is continuously affected by various environmental loadings such as wind, wave, and current. In general, waves are considered as one of the main external sources which induce dynamic behavior of the offshore floating structures. Therefore, fatigue damage and performance of the mooring lines should be evaluated based on their dynamic structural stress induced by the waves acting to the floating structures. In this study, fatigue damage and performance of the mooring lines for SFTs under severe wave conditions are analyzed using hydrodynamic analysis, Rainflow counting method, and Miner’s rule for obtaining dynamic stresses, treating the fluctuating stresses, and calculating the fatigue damage index, respectively.