The East China Sea Shelf Basin is an Upper Triassic-Middle Jurassic depression, Upper Jurassic-Cretaceous and Paleogene faulted-depressions, Neogene depression superimposed basin developed on the basis of the Pre-Mesozoic craton with rich hydrocarbon resources. It is located in the South China Block on the southeastern margin of the Eurasian Plate. However, in the deep layers (referring to the Upper Triassic-Cretaceous), due to the deep burial depth, complex regional tectonic background, geophysical field, and tectonic evolution, large changes in temperature fields, pressure fields and stress fields, strong geological tectonic transformation, and complex hydrocarbon accumulation process, a systematic evaluation on source rocks and oil and gas resource potential of the basin has not been carried out. Therefore, on the basis of previous studies, the drilling, seismic, and adjacent onshore data in the Southern East China Sea Shelf Basin (SECSSB) were comprehensively analyzed through regional seismic-stratigraphy and well-seismic calibration, three second-level tectonic sequences in the deep layers of the SECSSB were clarified: the Upper Triassic to Middle Jurassic, the Upper Jurassic, and the Cretaceous. The deep sequence framework and stratigraphic sequence evolution were established. Two sets of transgression-affected or marine shale source rocks mainly develop in the upper Triassic-Lower Jurassic and Lower Cretaceous were clearly pointed out. In addition, it is suggested that the total hydrocarbon generation capacity and average resource abundance in the deep layers of the SECSSB are relatively large and have considerable potential for petroleum resources, and it is an important area worthy of deep stratigraphic exploration for oil and gas exploration in the SECSSB in the future.