The evolution of the Yangtze River, and specifically how and when it connected to the East China Sea, has been hotly debated with regard to possible linkages with the so-called ‘Cenozoic Topographic Reversal’ (tectonic tilting of continental east China in the Cenozoic) and particularly the relationship to the uplift history of the Tibetan Plateau. Resolving this key question would shed light on the development of large Asian rivers and related changes in landforms and monsoon climate during this interval. Here, we use the magnetic properties of both Plio-Quaternary sediments in the Yangtze delta and of surficial river sediments to identify a key mid-late Quaternary switch in sediment source-sink relationships. Our results reveal a fundamental shift in sediment magnetic properties at this time; the upper 145 m of sediment has magnetic mineral concentrations 5 to 10 times higher than those of the underlying late Pliocene/early Quaternary sediments. We show that the distinctive magnetic properties of the upper core sediments closely match those of surficial river sediments of the upper Yangtze basin, where the large-scale E'mei Basalt block (2.5 × 105 km2) is the dominant magnetic mineral source. This switch in sediment magnetic properties occurred at around the Jaramillo event (~ 1.2–1.0 Ma), which indicates that both the westward extension of the proto-Yangtze River into the upper basin and completion of the connection to the East China Sea occurred no later than at that age.