Continental margins, which locate in the continental crusts and oceanic crusts, record the processes of the continental breakup and the ocean opening. It is important for the research on the geodynamics. The Cenozoic basins in deep water of northern margin of South China Sea located on the continental margin. The Cenozoic basin can be divided into three structural layers. They are rift layer, post-rift depression layer and post-rift subsidence of ocean basin layer. Rift basin layer performed as a series of graben and half graben. The character of post-rift depression layer is thick in the middle and thin on both side which looks like a disk. The thickness of post-rift subsidence of ocean basin layer changed greatly, it thick on the continental slope and thin on the ocean basin which showed the character as a “flexing basin”. The basin in deep water of northern margin South China Sea has experienced three evolution stages and showed the different geodynamic mechanisms. Influenced by the upwelling of the mantle, the basin mainly performed as horizontal extensional and formed the extensional structural styles in rift stage. In post rift stage, the basin subsided widely. In the third stage, the basin bended towards the South China Sea which controlled by the subsidence of ocean basin. The structural framework of continental shelf — continental slope — ocean basin is formed in the stage of ocean basin subsided. The activity difference of mantle material which under the basin of northern margin and the ocean basin is the main influence factors of the geodynamics.