Sediment transport characteristics during high floods in the upper reaches of the Yangtze River are the key factors that determine the sedimentation in the Three Gorges Reservoir, and are directly related to the service life and comprehensive benefits of the dam. According to long series flow and sediment data, the characteristics of sediment transport during high floods at Cuntan Station are analyzed. Results demonstrated that in the past four decades, the trend of seven-day flood volume at Cuntan station has not been distinct, whereas the seven-day sediment transport decreased significantly. The high-flood sediment transport has experienced a process from being dominated by rising flow, to a balance between rising and falling flows, and then to be dominated by the falling flow. Before 2013, runoff and sediment during the high-floods at Cuntan Station were mainly from the Jinsha River. After the operation of Xiangjiaba and Xiluodu projects, Cuntan Station witnessed fourteen flood events (peak flow above 30 000 m³/s) in total, of which only four came from the Jinsha River, nine from the Jialing River and one from the Minjiang River in terms of runoff source, while from the perspective of sediment source, nine were from the Jialing River, and the other five came from the Tuojiang River, Minjiang River, and Hengjiang River, which implied that Jinsha River is no longer the major source of sediment transport during the high floods. The research findings offer theoretical support for the Three Gorges Reservoir’s sand peak and silt reduction regulation, and provide a guarantee for the Yangtze River sediment control.