The deep-water natural gas hydrate reservoir in the South China Sea is characterized by shallow burial depth, low saturation and small gravel diameter, presenting in silty hydrate reservoir. Deep-water shallow unconsolidated formation poses a huge challenge of well borehole stability, which is essential for achieving a goal of the safety, success and efficient deep-water drilling. Therefore, based on the target area of formation conditions in the deep-water of the South China Sea hydrate testing, and the existing model that researched on well borehole stability, the paper mainly analyzed the mechanical properties of natural gas hydrate reservoirs and the law of complex multi-phase rheological decomposition, and studied on the rock mechanics and in-situ stress parameters of shallow rock. Established the criteria of deep-water shallow combined rock mass destruction and the well instability model during drilling process, as well as the determination rule for a safety drilling fluid density window for the whole well of deep-water shallow drilling, it came up with a evaluation method of well stability and the control plan for preventing instability in shallow drilling of deep-water natural gas hydrate formation, which are actually applied in the South China Sea natural gas trial production testing project. The results indicated that in the whole deep-water drilling process of shallow gas hydrate layer in the South China Sea, the borehole kept stability and got a smooth drilling process, which provided a certain reference and guidance for the subsequent exploration of complex well structure to test the deep-water hydrate.