The Shenhu gas hydrate drilling area is located in the central Baiyun sag, Zhu II depression, Pearl River Mouth basin, northern South China Sea. The gas compositions contained in the hydrate-bearing zones is dominated by methane with content up to 99.89% and 99.91%. The carbon isotope of the methane (δ13C1) are ?56.7‰ and ?60.9‰, and its hydrogen isotope (δD) are ?199‰ and ?180‰, respectively, indicating the methane from the microbial reduction of CO2. Based on the data of measured seafloor temperature and geothermal gradient, the gas formed hydrate reservoirs are from depths 24–1699 m below the seafloor, and main gas-generation zone is present at the depth interval of 416–1165 m. Gas-bearing zones include the Hanjiang Formation, Yuehai Formation, Wanshan Formation and Quaternary sediments. We infer that the microbial gas migrated laterally or vertically along faults (especially interlayer faults), slump structures, small-scale diapiric structures, regional sand beds and sedimentary boundaries to the hydrate stability zone, and formed natural gas hydrates in the upper Yuehai Formation and lower Wanshan Formation, probably with contribution of a little thermogenic gas from the deep sedments during this process.