The geomorphological stability and ecological environment of megadeltas worldwide are of vital importance for their sustainable development. Deltaic hydro-morphodynamics is extremely sensitive to high riverine flow due to reduced sediment supply. However, the morphological evolution and response of deltas under high riverine flow have remained inadequately quantified. As one of the typical megadeltas, the Yellow River Delta (YRD), is becoming increasingly sensitive to environmental changes and intensified human interventions. In this study, a numerical model and field data were used to investigate the hydrodynamic changes and morphodynamic evolution induced by extreme river discharge in the YRD. The numerical experiments with different runoff scenarios reveal that high-energy riverine floods can cause significant hydrodynamic changes in bed shear stresses, water levels, and flow velocities, particularly in the abandoned river mouth. Moreover, it enhances the ebb-dominated tidal asymmetry, which considerably intensifies fluvial sediment resuspension and transport processes. The results also show high-energy riverine floods in the flood seasons trigger severe erosion in the Yellow River submerged delta, with a net erosion volume reaching −0.07 × 108 m3/year. The hydrodynamic increment in the abandoned river mouth is more significant, and therefore, severe erosion occurs, with the maximum erosion thickness reaching 7 m. These findings highlight the role of high riverine floods on the hydro-sediment dynamics of large river deltas under a sediment starvation condition.