Abstract: The global climate, oceanographic and tectonic processes can affect the stability of gas hydrate, resulting in highly dynamic changes of seafloor environments. A coupled seafloor/borehole observatory system can be used to monitor the chemical, microbiological and physical data to achieve a better understanding of these changes, the carbon cycling and resource exploitation in gas hydrate-bearing continental margin. A borehole monitoring system for marine gas hydrates was designed conceptually and discussed about its relatively key problems in its development. While drilling and deploying the borehole instrumentations, borehole safety should be considered and geomechanical stability of hydrate-bearing formations should be assessed whether it can support the borehole instrumentations. Some drilling and completion methods will be taken to reinforce and stabilize the weak and friable hydrate-bearing formations, which can realize a long-term observation. Finally, some suggestions were proposed and discussed for carrying out the borehole hydrate observatory system in the South China Sea in the future.