Abstract: The combined effect of typhoon storm surges and fluvial floods poses a significant threat to estuarine regions. Based on topographic data of the Yongjiang Estuary before and after Typhoon Fitow (the 23rd severe typhoon in 2013), this study investigates the hydro-sediment dynamic variation laws under compound flood conditions using a three-dimensional hydro-sediment mathematical model and sediment flux mechanism decomposition. The results indicate that fluvial flood is the primary driving force behind the channel evolution of the Yongjiang Estuary. It reshapes the estuarine dynamic structure by raising water levels, suppressing flood tidal currents, and enhancing ebb tidal currents, thereby controlling the pattern of sediment transport to the sea and the "flood scouring" evolution trend of the channel. Storm surge setup exerts a buffering effect on the flood dynamic process by elevating the reference sea level, weakening the intensity of flood-induced modifications to the estuarine dynamic environment. A key finding reveals that the interaction between floods and storm surge setup is not a linear superposition; their coupling leads to nonlinear response characteristics such as the migration of sediment transport balance points and anomalies in sediment transport flux.