Pockmarks, as depression morphology related to fluid escape on the seafloor, are revealed by 3D seismic data on the northwestern South China Sea (SCS) margin. The pockmarks can be classified into two groups based on their various shapes in plan view: the circular group and the elongating group. These pockmarks in the study area could be defined as mega-pockmarks because their maximum diameters can reach to 7.5 km. They commonly develop more than one crater, which are called the central crater and the secondary crater. The seismic data illuminated their complicated internal architectures in the subsurface, as well as their evolution periods, such as the initiation stage, mature stage, and abandonment stage. According to the buried structures and their genesis mechanism, mega-pockmarks could be classified into linear faults-associated pockmarks and volcano-associated pockmarks. The linear fault-associated pockmarks root on the top Middle Miocene, where the linear faults are distributed. The linear faults on the top of fluid reservoir in Middle Miocene act as conduits for fluid seepage. The fluid seepage is driven by the break of balance between the hydrostatic and pore pressure. When the fluid seepage initiates, they will migrate along the linear faults, making the linear feature of pockmarks on the seafloor. Thermogenic gas from deep intervals and biogenic gas from shallow intervals may be fluid sources for the genesis of pockmarks. However, the volcanic activities control the genesis and evolution of volcano-associated pockmarks. Volcano-associated pockmarks root on the craters of volcanoes. The volcanoes underneath the pockmarks provide volcanic hydrothermal solutions, such as phreatomagmatic eruptions through the volcanic craters. The confined fluid seepages make the pockmarks exhibit a more circular shape on the seafloor. Long-term, multiepisode fluid expulsions generate the complicated internal architecture that leads to multicratered mega-pockmarks on the northwestern margin of SCS.