A thorough magnetostratigraphic chronology of the Yangtze River Delta is problematic due to coarse-grained (i.e., poorly magnetized) deposits and sedimentary discontinuity. This study presents cosmogenic nuclide data which facilitate ²⁶Al/¹⁰Be burial dating to determine the absolute age of horizons from four previously reported long onshore boreholes in the Yangtze Delta region that record sediment provenance change to the Yangtze River. Dates obtained close to the provenance change horizons in boreholes RGK15 and ZKJ39 from the northern delta were 4.99 (+1.26/−0.81) Ma and 4.74 (+0.94/−0.70) Ma, the oldest radiometric ages of borehole sediments yet to date. The provenance change horizon in boreholes LQ19 and LQ11 in the southern delta were dated to 0.94 (+0.17/−0.16) Ma and 0.57 ± 0.17 Ma, respectively. These new ages combined with previous lithofacies and provenance studies imply that the proto-Yangtze River first entered the northern delta prior to ~5 Ma, then migrated gradually southward to the present estuary location after 0.94 Ma and moved even further south at 0.57 Ma. The southward migration history of the proto-Yangtze River channel sheds lights not only on the tectonic subsidence widely occurring on the east China coast during the Quaternary, but also on the somewhat controversial connection history of the Yangtze River to the East China Sea.