Slamming-induced whipping has been recognized as a key contributor to fatigue damage of large ships operating under severe sea states. However, accurate prediction of whipping responses remains challenging because of complex nonlinear fluid–structure interactions. This study aims to investigate the characteristics of slamming-induced whipping and quantitatively analyze its influence on the fatigue damage of an ultra-large container ship. A three-dimensional fully nonlinear time-domain hydroelastic method, in which the boundary element model is coupled with a Timoshenko beam model, is employed to predict the slamming-induced whipping responses. Segmented model tests in long-crested irregular waves are conducted to provide wave loads of hull girders under severe sea states. The total and wave-frequency vertical bending moments are separated by the fast Fourier transform, and their statistical characteristics are evaluated through probability distributions. Fatigue damage is assessed on the basis of the rainflow counting method and the Palmgren–Miner cumulative damage rule. The contribution of high-frequency whipping responses to fatigue damage is quantitatively evaluated using a fatigue damage factor. It is demonstrated that slamming-induced whipping can significantly amplify fatigue damage by increasing stress amplitudes and cycle counts, particularly under high forward speeds and severe sea conditions. The findings provide a reliable reference for the fatigue design and safety assessment of ultra-large container ships.