The polygonal faults in southern Xisha Offshore, South China Sea, were first discovered. On the basis of the 3D seismic data and the analysis of the controlling factors for polygonal faults development, it is concluded that the fine grained sediment strata from far source is the favorable development site in upper structure layer of Xisha Offshore. At the same time, channel sandstone, diagenesis and tectonism affected their development and distribution. Polygonal faults, combining with the deep tectonic fault, provided channels for fluid migration from deep hydrocarbon source rocks to the upper reservoir, or continued upward to the shallow strata to form natural gas hydrates.