Quantitative research regarding the effects and contribution rates of both natural processes and human interventions on the long-term evolution of the Yangtze Estuary is currently insufficient. To address this, we employ the Mann-Kendall (M-K) test to analyze hydrological changes and utilize bathymetric maps from 1958 to 2019 to quantify erosion and deposition patterns. Subsequently, combined with the empirical orthogonal function (EOF) to separately identify the top three control factors and elucidate spatiotemporal characteristics of the main factors controlling the Yangtze Estuary's morphological evolution. The results showed that sediment load and runoff consistently rank within the top three with respective mean contribution rates of 40.5% and 19.4%. Sediment load prevails as the first control factor across all regions except for the North Passage, which experienced a transition from natural dominance to human domination in 1998. Notably, extremely events like the 1998 flood occupied more eigenweighting in the short term and progressed in ranking due to the strong channel-forming capacity. Regarding escalating human interventions, estuarine engineering projects affect estuarine shoals following initial deposition and subsequent erosion patterns. However, their influence tends to wane post-completion, often surpassed by natural processes. Specifically, since 2010, continuous navigation channel dredging has governed the morphological evolution of the North Passage. Additionally, sand mining targeting the Ruifeng Shoal has driven the post-evolution dynamics of the South Channel as the second control factor. Overall, this study enhances our understanding of the coupling driving mechanisms involving both natural processes and human interventions, thereby enabling improved strategies for future sustainable management in estuarine environments.