Based on high-resolution 3D seismic data, a sort of polygonal fault systems has been identified in Pliocene-Pleistocene strata in Lower Congo Basin. Within the seismic sections, the polygonal fault systems are characterized by small extensional faults,which develop in pelagic or hemipelagic sedimentary environment with fine-grained mud-dominated sediments. Within the seismic-time coherent slices, polygonal shapes are identified in map view. The orientations of the polygonal faults are almost isotropic, which indicatesa non-tectonic origin. In an identical highly-faulted interval, it is characterized by dense in the upper and rare in the lower. The development mechanism for the polygonal fault systems is inferred to be that due to the volumetric contraction induced by syneresis during early burial of compaction of fine sediments at the top, dense layers formed and resisted against the drainage of fluid out from undercompacting muds tone in the lower, which gradually resulted in polygonal faults. With evolution of strata, new polygonal faults could develop under previous polygonal faults and simultaneously the upper polygon faults would be active once again. The factors dominating the development of polygonal fault systems are mainly the sizes of sediment grain and the composition of minerals. With decreaing grains and increasing montmorillonite, polygon faults will develop further in the extent. Polygonal faults not only can be as pathways of hydrocarbon migration but also form overpressure that seals hydrocarbon to escape.