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Deltaic areas and marginal seas are important archives that document information on regional tectonic movement, sea level rise, river evolution, and climate change. Here, sediment samples from boreholes of the Yangtze Delta and the modern Yangtze drainage were collected. A quantitative analysis of detrital zircon morphology was used to discuss the provenance evolution of the Yangtze Delta. This research demonstrated that a dramatic change in sediment provenance occurred in the transition from the Pliocene to Quaternary. Zircon grains in the Pliocene sediments featured euhedral crystals with large elongation (>3 accounted for 13.2%) and were closely matched to tributary samples in the Lower Yangtze (>3 accounted for 11.3%), suggesting sediment provenance from the proximal river basin. However, most detrital zircon grains of the Quaternary samples exhibited lower values of elongation and increased roundness (rounded grains were 9.4%), which was similar to those found in the modern Yangtze mainstream (rounded grains were 12.5%) and the middle tributaries (rounded grains were 7.0%). The decrease in zircon elongation and improvement of its roundness in the Quaternary strata implied that the Yangtze Delta received sediments of different provenance that originated from the Middle-Upper Yangtze basin due to the uplift of the Tibetan Plateau. Statistical analysis of detrital zircon morphology has proven useful for studying the source-to-sink of sediments.