The northern South China Sea (SCS) experienced a significant transition from a lacustrine to marine environment in the Paleogene, and its deep-water basin of Zhu-II Depression is in particular extensively studied due to its richness in oil and gas resources. However, limited number of boreholes in the deep-water area has long constrained a better understanding on the provenance of the Paleogene strata and the associated sediment transport processes. In this study, detrital zircon U-Pb ages and three-dimensional (3D) seismic-reflection data were systematically employed to investigate the “source-to-sink” pathways and interplay of longitudinal and transverse sediment dispersal. Our results indicate that the Zhu-II Depression sediments of the northern SCS were predominantly derived from the surrounding nearby paleo-uplifts in the early and middle Eocene. A significant provenance shift took place in the late Eocene, when the local paleo-uplift source was replaced by a distant source from the western SCS. Sediments were transported from west to east by the “Kontum-Ying-Qiong River” as a longitudinal dispersal. In the Oligocene, the “Kontum-Ying-Qiong River” delivered large amounts of sediments from Central Vietnam to the eastern part of the northern SCS. Meanwhile, the Pearl River gradually evolved through regional tectonic processes and influenced the deep-water area of Zhu-II Depression as a transverse dispersal. Sediments from both “Kontum-Ying-Qiong” and Pearl Rivers converged and deposited as deep-water deltas in the Zhu-II Depression. This dual provenance system in the northern SCS deep-water area was featured by the interplay between longitudinal and transverse sediment dispersal. It was largely controlled by the tectonic-palaeogeographic pattern inherited from the Mesozoic arc system.