The discovery of natural gas field in the deep water area of the northern margin of the South China Sea (SCS) made it as one of the hot areas in global oil and gas exploration. Comparative studies of deepwater basins in the world and the SCS adjacent continental shelf areas show that the deepwater area of the northern SCS is featured by unique petroleum geology as follows: tectonic transition from the active margin in Yanshan period to Cenozoic passive margin accounts for the complex evolution and basin formation mechanism. The thermal regime is hotter in the deepwater slope area and overpressure phenomenon is generally found in the depressions there, along with ambiguous hydrocarbon formation process. Due to the long distance from the provenance and lack of the material flux from the big rivers, this area is with distal sedimentation. No salt related tectonics is found in this area. All the phenomena mentioned above suggest its unique hydrocarbon formation. Additionally, the topography in deep water area of the northern SCS is rugged, along with multiple volcanoes, which undoubtedly arises difficulties for geophysical data acquisition and process. In a conclusion, the oil and gas exploration in deep water areas in SCS should takes the successful experiences in any other deep water areas in the world as reference, and enhance the basic research on its structural and petroleum geology; meanwhile, the new geophysical technologies for deep water environment are also need to promote the progress of oil and gas exploration.