The late Cretaceous to early Oligocene strata in the northern continental margin of the South China Sea (SCS) are significant for understanding the contemporaneous continental rifting of the margin prior to the opening of the central SCS oceanic basin. Using new seismic and drilling data, combined with previous results, we have identified three episodes of rifting from the late Cretaceous to early Oligocene based on analyses of major unconformities, tectonostratigraphic units, and sedimentary facies. The first episode of rifting that occurred only in the Pearl River Mouth (PRM) basin during the late Cretaceous to Paleocene is observed. During the early to middle Eocene, littoral-shallow lacustrine and fan-delta facies were distributed in some faulted half-grabens in the Qiongdongnan (QDN) basin, while deep lacustrine deposits widely developed in the PRM basin. During the late Eocene to early Oligocene, marine transgression propagated from the southeast into the QDN, southern PRM, and Taixinan basins. We have inferred that late Cretaceous to the middle Eocene rifting is characterized by uniform lithospheric stretching related to the retreat of the paleo-Pacific subduction zone, whereas the late Eocene to the early Oligocene rifting controlled by multiple factors is characterized by depth-dependent lithospheric extension. It is the differential rifting process that led to the differentiation in the types and distribution of source rocks in the basins of northern SCS margin.