Abstract: Driven by global changes and human activities, the sediment source/transport, and riverbed erosion and deposition pattern of the Yangtze River Basin are undergoing continuous adjustments, which influence both magnitude and property of fluvial sediment to the estuary. In order to explore sediment transport and correlated topographic changes of the Yangtze River Estuary within 40 years in response to variations of fluvial sediment discharge from the upstream basin, this study uses sediment grain size trend models and multi-year zonal analysis methods to predict temporal and spatial variations of morphological changes within the Yangtze Estuary, based on grain size data and topographic data from 1980 to 2020. The results show that sediments converge toward the center of the channel within the northern branch, and a deposition center forms close to the south and north channel diversion area within the southern branch, consistent with the morphological changes between 2012 to 2020 calculated from sea maps, validating the effectiveness of the grain size trend model in predicting morphological changes within the Yangtze River Estuary. The results of the multi-year zonal analysis show that: 1980—2003 was characterized by a high volume of fluvial sediment discharge, and the entire estuary area was dominated by deposition with slightly finer sediment. Fluvial sediment discharge experienced a rapid decrease from 2003 to 2012, while the estuary area was still dominated by deposition before 2009 with similar grain size. 2009—2012, however, was a transitional period when erosion and sediment coarsening started to appear out of the estuary, although limited to small areas. From 2012 to 2020, large-scale erosion and grain size coarsening occurred widely in the estuary, and a significant correlation was found between the particle size and the magnitude of erosion. Our study shows that high-resolution zonal analysis can effectively catch the local morphological change signals in the Yangtze River Estuary. In the past 40 years, the Yangtze River Estuary has changed from deposition-dominant mode to partially erosion mode, and it may face continuous coastal erosion in the future.