The Zhu III Depression, situated in the northern Pearl River Mouth Basin, features a complex fault system composed of NE–SW-, nearly E–W-, and NW–SE-oriented faults. However, there is limited research on NW-trending faults, especially regarding their formation mechanisms. Through structural analysis of 3D seismic profiles, we have revealed the geometric and kinematic characteristics of NW-trending faults and categorized them into three types based on their formation mechanisms: extensional fault, dextral transtensional fault, and sinistral strike–slip fault. The extensional faults predominantly developed as boundary faults during the rifting I period, caused by tectonic inversion of the NW–NWW-trending basement faults since early Eocene. The transtensional fault resulted from the dextral strike–slip motion of the NE-trending basin-controlling faults since late Eocene, under the regional dextral extension stress setting. The sinistral strike–slip faults have been dominant during the post-rifting period since early Oligocene. This is due to the sinistral shearing action related to the southeastward lateral extrusion of the Indochina Block and slab pull southward by subduction of the proto-SCS. The NW-trending faults controlled the development of local tectonics and structures, the depocenter migration during the rifting period, and the trapping, migration, and preservation of oil and gas.