<p>Nonlinear fluid oscillations in the narrow gap between two side-by-side, nonidentical barges are numerically investigated under two different initial conditions, i.e., initial calm and post-transfer conditions, based on a two-dimensional fully nonlinear potential flow solver. This study aims to explore the nonlinear resonance hysteresis of fluid oscillations in the gap during ship-to-ship transfer operations. Nonlinear responses under initial calm conditions are first elucidated within a broad wave parameter space, primarily concerning the phase state regimes, i.e., phase dynamics. Phase locking, trapping, and drifting states are thoroughly clarified, providing corresponding region maps. The full-time nonlinear simulation of the transfer process for ship-to-ship operations is subsequently performed to identify the nonlinear resonance hysteresis in the gap resonance problem. The results show that nonlinear hysteresis is fundamentally governed by the phase dynamic states. The transition from the phase locking to phase trapping or phase drifting states indicates a shift from a stable, periodic state to one that is sensitive to initial conditions, thereby leading to nonlinear resonance hysteresis. The significance of nonlinear hysteresis in ship-to-ship operations is emphasized for both primary and super-harmonic resonances in terms of the amplitude–frequency responses, higher-order harmonics, and time-varying wavelet energy spectra. The physical insights gained from this study provide a deeper understanding of the nonlinear resonance hysteresis involved in practical ship-to-ship transfer operations.</p>