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The process of Cenozoic sea-land changes in the northern South China Sea (SCS) controlled the sedimentary filling pattern and played an important role in the petroleum geological characteristics of the northern marginal sedimentary basins. Under the control of the opening process of the SCS, the northern SCS Cenozoic transgression generally showed the characteristics of early in the east and late in the west, and early in the south and late in the north. The initial transgression occurred in the Eocene in the Taixinan Basin (TXNB) of the eastern SCS, while the transgression occurred until the Pliocene in the Yinggehai Basin (YGHB) of the western SCS. International Ocean Discovery Program (IODP) expeditions (Expeditions 367/368) revealed that the initial transgression of the SCS basin occurred at approximately 34 Ma, which was the initial opening time of the SCS. The period of drastic changes in the sedimentary environment caused by large-scale transgression corresponded to the opening time of the southwestern subbasin (approximately 23 Ma), which also represented the peak of the spreading of the SCS. The sea-land transition process controls the distribution of alternating continent-marine facies, marine facies source rocks and reservoirs in the basins. The marine facies source rocks of the basins in the northern SCS have a trend of gradually becoming younger from east to west, which is consistent with the regional process of gradual transgression from east to west. Regional sea-level changes were comprehensively influenced by SCS opening and global sea-level changes. These processes led to the early development in the east and south and late development in the west and north for the carbonate platform in the SCS. Carbonate platforms form another type of “self-generating and self-accumulating” oil-gas reservoir in the northern SCS. The sea-land transition controlled the depositional filling patterns of different basins and laid the foundation of marine deposits for oil and gas resources. The source-reservoir-cap assemblage in the northern SCS was controlled horizontally by provenance supply and sedimentary environmental changes caused by sea-land transition and vertically by the tectonic evolution of the SCS and regional sea-level changes.