Abstract: Although previous many studies on the pre-Cenozoic stratigraphy of the Pearl River Mouth Basin have been done, there is still a lack of unified understanding of the original structural pattern of the basin. With available high-precision 3D seismic data, we implemented “qualitative + quantitative” comprehensive identification technology for the recognition of pre-existing fractures, by which 583 pre-existing fractures in the pre-Cenozoic basement of Huizhou Sag and Panyu 4 Depression in the Pearl River Mouth Basin were identified at the end. According to whether the fault runs through reflector Tg （the seismic horizon at the basement） and the fault dip angle, we divided the pre-existing fracture into four types: high-angle joint, low-angle joint, high-angle re-active fault, and low-angle re-active fault. In addition, according to the fractures’ strike, we classified the pre-existing fractures into two groups: NW-NWW and NE-NEE. From the Late Jurassic to Early Cretaceous, the paleo-Pacific Plate subducted into the South China Plate perpendicularly in NW direction and formed NE-NEE thrust faults; in the Late Cretaceous, the paleo-Pacific Plate subducted into the South China Plate obliquely and produced a sinistral compressive stress field, resulting in the formation of NW-NWW thrust faults. These pre-existing fractures control the overall structural pattern of the Pearl River Mouth Basin, and provide an important support to the future study on the subsequent evolution of the basin.