Great attention has been paid to natural gas hydrate system by petroleum geologists recently. The migration and accumulation system of natural gas hydrate fits well into the theory of petroleum system "from source to trap". The formation of natural gas hydrate system depends on the temporal and spatial coordination of a rich source, a favorable gas migration conduction system, and a high pressure and low temperature stability zone. In order to explore the basic characteristics of natural gas hydrate system in the northern South China Sea, based on the natural gas hydrate petroleum system theory as well as the gas hydrate exploration data, this paper dissected and summarized the basic geological conditions and controlling factors of gas hydrate migration and accumulation in the Shenhu area, Dongsha area and Xisha Trough on the northern slope of the South China Sea. Moreover, different gas hydrate migration and accumulation models in three areas have been established, especially for the biogenic gas leakage gas hydrate. We hope this paper can provide references and guidance in some sense for accelerating and promoting the exploration of gas hydrate in South China Sea.