A combination of detrital zircon U-Pb geochronology and rare earth element geochemistry was employed to investigate the “source to sink” pathways of Eocene–lower Miocene strata in the northern South China Sea (SCS) taking into account the evolution of the surrounding drainage systems in comparison to the basin sediments. Drastic provenance transformation on the SCS sedimentary patterns has been first discovered that source of Central Vietnam was replaced by Pearl River networks. Rapidly changing local provenances of different source rocks were discerned during Eocene and early Oligocene times. Briefly, the Pearl River drainage system gradually evolved by regional tectonic processes into the present scale and exerted its influence on the northern SCS basins. During early Oligocene, only limited areas received sediments from Pearl River tributaries on the South China continent, while the majority of the southern areas were controlled by the Central Vietnam provenance before the late Oligocene. After the early Miocene, significant amounts of sediment from the inner South China continent were transported into northern SCS basins by the western Pearl River tributaries. Meanwhile, an impressive “Kontum-Ying-Qiong” river system (K-Y-Q) had delivered huge amounts of sediments from Central Vietnam mafic-to-ultramafic source rocks to the regions farther east since the early Oligocene or even Eocene. This remarkable K-Y-Q traversing the whole Qiongdongnan Basin was gradually replaced by a transport system from the adjacent Hainan Island, in modern-day China, providing acidic detritus after the early Miocene. Admittedly, Tethyan subduction beneath Sundaland makes the paleo-reconstruction work tough and elusive. However, we laid the emphasis on possible basin depositions to unravel the mystery and our discovery of the impressive conduit from Central Vietnam of the Indochina Block, transferring abundant basic sediments derived from the Indosinian event, surely would be of remarkable significance on research of (1) paleo-geographical evolution by Tethys-southern Eurasia Plate collisional effects and (2) tectonic reconstruction for the entire southeastern margin of the Eurasian continent.