Abstract: On the northern slope of the South China Sea, both the genesis and distribution of energy resources, such as deepwater oil and gas and gas hydrates, show a spatial-temporal coupling pattern and genetic relationship with their crustal and lithospheric deep structures, especially the types of shallow crustal sedimentary basins and basin-forming mechanisms. They are also the hot focus and key concerns among the oil and gas exploration researchers and academic scholars. Based on the geological and geophysical data collected from the marine geological surveys and oil and gas exploration and development sectors, the basic geological characteristics of deep lithospheric crust tectonic units along the northern margin of the South China Sea are analyzed in this paper. Based on the new model of crustal detachment and thinning along the continental margin by extension, we studied the spatial and temporal coupling relationship between the deep crustal structures and the deep-water basins, and discussed the genesis of deep-water basins and its resource effects as well as their relationship with deep-water oil and gas and hydrate accumulations. It is predicted that the oil and gas resource potential and exploration prospects of deep-water and ultra-deep-water basins in the continental slope-ocean-contilental transitional zone are obviously better than those in shallow water basins on the continental shelf. The potential of natural gas hydrate is also huge in deep-water and ultra-deep-water basins. In conclusion, the deep water basins are important strategic replacemnt area for sustainable development of offshore oil and gas exploration and development in China.