This paper presents a method for estimating the sectional loads along ship hull girder in real-time by combining a Kalman filtering algorithm and a mode superposition method, as part of digital twining system. The developed method is applied to a full-scale measurement on an 8600 TEU container ship and the strain signal at several locations is used as inputs to estimate hull deformation and external loads. The stress distribution at deck level due to vertical bending moment, and horizontal and torsional moment distributions are presented and discussed. Then, the method is extended for identifying whipping and springing events. It is justified by comparing with other methods that have been accepted so far. The effects of whipping and springing on fatigue damage are respectively analyzed by separating the wave-induced vibrations into whipping and springing. It is shown that the fatigue damage caused by the wave-induced vibrations is significant and the fatigue damage caused by springing is equivalent to, or even larger than the one by whipping.