The East China Sea Basin is located on the southeastern edge of the Eurasian Plate. Since the Mesozoic era, the basin formation and evolution processes have been superimposed with the multi-period oceanic subduction of the paleo-Pacific Plate and multi-structural systems interacting with the Indo–Australian Plate, Pacific Plate, and Eurasian Plate. As previous studies have mainly focused on the Cenozoic era, the basin prototype, tectono-sedimentary characteristics, and key factors controlling hydrocarbon accumulation during the Mesozoic era have always been hotspots for research and scientific questions as part of a “New horizon” for oil and gas exploration in the East China Sea Basin. Based on the latest data from seismic, drilling, and onshore-offshore comparison studies in the Southern East China Sea Basin (SECSB), this study explored the key factors controlling the oil and gas generation, migration and accumulation, and exploration direction of the Mesozoic hydrocarbon accumulation by employing onshore-offshore comparisons, seismic stratigraphy, and structural-sedimentary evolutionary reconstruction. The results showed that three regional unconformities and seven seismic sequences formed during the Mesozoic period in the SECSB. The evolution since the Mesozoic era included the formations of a basement by the passive continental margin before the Late Triassic, the Late Triassic–Middle Jurassic depression of the active continental margin, and the Cretaceous faulted basins at continental margins. It is proposed that 1) the early basal NE-trending structural framework controlled the structural pattern of the Mesozoic basin and the macro-hydrocarbon properties, according to which the Cretaceous should be dominated by oil, and the Upper Triassic-Middle Jurassic should be dominated by gas; 2) two sets of source rocks (i.e., Upper Triassic-Lower Jurassic mud shale and Lower Cretaceous mudstone source rocks) were deposited, which formed the material basis for hydrocarbon accumulation and the source-reservoir-seal combinations during two stages of basin evolution in the Mesozoic era; 3) the East China Sea Basin has experienced at least seven tectonic movements since the Mesozoic period, including the Keelung, Yushan, Yandang, Oujiang, Yuquan, Longjing, and Okinawa Trough movements, among which the Keelung, Yushan, and Yandang movements dominated the formation and accumulation of early oil and gas, and the adjustment, transformation, and re-establishment of early reservoirs was accomplished by the Longjing Movement; and 4) the Minjiang Slope and the Taipei Turning Belt are the main petroleum exploration areas in the Mesozoic basin, in which the Cretaceous should be the main target layer in the east of the basin, and the Upper Triassic–Middle Jurassic in the west.