Different types of bottom simulating reflectors (BSRs), along complex morphologies of gas hydrates, have been revealed in the northern South China Sea. They occur in different tectonic-sedimentary settings. Fracture-filling and pore-filling gas hydrates are widely discovered above different types of BSRs by drillings and indicated by chimney-like or high amplitude reflections on seismic profiles. The existence of structure II gas hydrates, the coexistence of gas hydrates and free gas, the recently active gas hydrate systems, and the extensive distributed shallow gas are all due to the supply of thermogenic gas and relatively high flux of fluid migration. The pathways, such as faults, fractures, thrust faults, diapir and gas chimneys, which are formed by magmatism, intrusive structures, overpressure, or compressional tectonic forces, play important roles in vertical fluid migrations, particularly in areas where multi-stages mass transport deposits distributed. The differences in the tectonicsedimentary settings are suggested to account for the shifts of the BSRs in the northern South China Sea. The tectonic activities control the development of fluid migration pathways, and the reservoir plays a crucial role in the accumulation of various types of gas hydrate. A comprehensive understanding of these differences in gas hydrate occurrences and their key geological controls can contribute to the exploration for gas hydrates in the future.