Globally, over the past few decades, extreme river channel deformation has been observed downstream of dams. Specially, estuarine channel deformation and its response to natural and anthropogenic factors are key issues influencing channel regulation and prediction of long‐term stability in large estuarine deltas. Herein, bathymetry data for the upper reaches of the Yangtze Estuary (YE), China was collected for the years 1995, 2003, 2008, 2013, and 2019 to analyze the channel deformation process. Our findings show that the total erosion volume was approximately 11.22 × 108 m3, an equivalent of 15.7 × 108 t of sediment assuming a bulk density of 1.4 t/m3 for the riverbed material during 1995–2019. Meanwhile, the annual erosion rate is 0.63 Mt/year in 1995–2019, and the annual erosion rate is 0.90, 0.12, 0.40 Mt/year in 1995–2003, 2008–2013 and 2013–2019, respectively. Meanwhile, the annual deposition rate is 0.7 Mt/year during 2003–2008. Further analysis indicated that continuous reduction of the sediment load due to the construction of dams (e.g., the Three Gorges Dam) in the basin was a key factor influencing channel erosion over the past 24 years. The channel deformation process was characterized by severe erosion during 1995–2003, a deposition period during 2003–2008, a dynamic equilibrium period from 2008–2013, and an erosion period after 2013. Due to floods with maximum peak discharge lower than 70,000 m3/s, despite the annual sediment load is reduced, the channel deposition phenomenon occurred in 2003–2008. The channel changed from a depositional system to an erosion system during 2008–2013. After 2013, the channel was dominated by extensive erosion, severe local deposition, or severe local erosion as a response to anthropogenic interventions. These findings are of great significance to river management and regulation, as well as to the navigational safety.