Based on the new seismic and drilling data and the recent related research results, this paper systematically analyzes the diversity and complexity of evolution process of crustal lithosphere structure and basin structure in the Pearl River Mouth Basin on the northern margin of the South China Sea. Three types of detachment faults of different structural levels exist: crust-mantle detachment, inter-crust detachment and upper crust detachment. It is considered that different types of extensional detachment control different subbasin structures. Many fault depressions controlled by upper crust detachment faults have been found in the Zhu I Depression located in the proximal zone. These detachment faults are usually reformed by magma emplacement or controlled by preexisting faults. Baiyun-Liwan Sag located in the hyperextension area shows different characteristics of internal structure. The Baiyun main sag with relative weak magmatism transformation is a wide-deep fault depression, which is controlled by crust-mantle detachment system. Extensive magmatism occurred in the eastern and southwest fault steps of the Baiyun Sag after Middle Eocene, and the crust ductile extensional deformation resulted in wide-shallow fault depression controlled by the upper crust detachment fault. Based on the classical lithosphere extensional breaking and basin tectonic evolution in the Atlantic margin, it is believed that the magmatic activities and pre-existing structures in the Mesozoic subduction continental margin background are important controlling factors for the diversified continental margin faulted structures in the northern South China Sea.