The recent drilling results of marine gas hydrate reveal that the shallow sediments in a hydrocarbon rich depression are the potential places for gas hydrate formation when hydrocarbon rich depression is of preferential temperature, pressure and other conditions for hydrate accumulation. However, our investigation found that the gas compositions and carbon isotope of hydrates in shallow strata show biogenic or mixed biothermogenic characteristics, but no thermogenic, although hydrocarbonrich depressions are of excellent potential of hydrocarbon generation and discharge and enough supply of thermogenic gas, both of which can provide sufficient gases for hydrate formation. Two gas hydrate expeditions (GMGS 01&03) were carried out in the Baiyun Depression, South China Sea (SCS), as organized by Guangzhou Marine Geological Survey in 2007 and 2015, respectively. Compared with the results of no or minor contribution of thermogenic gas to hydrate formation at the drilling sites in 2007, higher contents of ethane and propane (up to 5%) in hydrates were detected at the sites drilled in 2015, providing direct evidence that deep thermogenic gas was a significant source for shallow hydrate formation. Geochemical results of industrial boreholes in the Baiyun depression indicate that part of thermogenic gas would migrate from hydrocarbon source rocks through faults, diapirs and gas chimney to shallow strata to form natural gas hydrate, although deep hydrocarbon gas escaped obviously from the reservoir due to the Dongsha movement in the late Miocene. In this paper we discussed the factors associated with hydrate formation, based on the model of vertical coupling relation of “deep hydrocarbon source rockinterconnecting migration channelshallow gas hydrate formation” in the two Shenhu hydrate drilling areas, and it is found that the type and permeability of gas migrating path might be the reason for the difference in gas source in the two areas. For the 2007 drilling area, long migration of deep thermogenic gas along low energy channels might cause differentiation of gas compositions and fractionation of carbon isotope, resulting in that the gas shows more “biogenic gas” features. 2015 drilling result found that through well developed faulting and diapir structures, the deep gases can be transported efficiently to shallow sediment layers in which gas hydrate formed, without oblivious change in chemical and isotopic composition.