The mode and tempo of Cenozoic fluvial input into the South China Sea by Asian rivers were strongly controlled by tectonically induced topographic changes and landscape development that resulted in repeated river captures and reversals. New Nd isotope and U‐Pb detrital zircon data from clastic sedimentary sequences in the northern South China Sea display secular variations reflecting significant changes in the compositions of fluvial sediment as well as changes in source rocks. The oldest, Eocene‐Oligocene (before ∼25 Ma) clastic rocks of the South China Sea contain sediments with ɛNd values of −5 to −7.5 and detrital zircons of Cretaceous, Jurassic, and Permo‐Triassic, all derived from southern Cathaysia. The Oligocene‐Middle Miocene (∼25–11 Ma) sediments in the South China Sea strata display ɛNd values of −12 to −14 and Archean, Proterozoic, and Paleozoic detrital zircons, suggesting northern Cathaysia and/or the Yangtze Blocks as their provenance. The headward expansion of the Pearl River and reversal of the Middle Yangtze River correlates with the opening of the South China Sea and growth of the eastern Tibetan Plateau at ∼25 Ma. Further uplift of the eastern Tibetan Plateau and the Wuyi‐Nanling Mountains in SE China around 11 Ma reshaped the landscape and caused another phase of erosion—pattern adjustment and drainage—divide migration in East Asia, leading to the establishment of the modern fluvial systems of the Pearl, Minjiang, and Lower Yangtze Rivers.