Based on the theory of structural analysis, the characteristics and structural patterns of subtle faults are studied using 3D seismic data of the Bohai Sea to analyze the development process and origin of the subtle faults. A method of identifying subtle faults is proposed, forming a complete system for analyzing origins of subtle faults in the Bohai Sea. The complex strike-slip fault patterns under the strike-slip and extension stress background, diverse formation rocks, and strong neotectonic movement are the reasons for the development of subtle faults. According to the tectonic origin and development location, the subtle faults in Bohai Sea can be divided into 12 types in the three categories of strike slip dominant, extension dominant and strike slip and extension composite, and the different types of subtle faults occur in different regions of the Bohai Sea. Unreasonable variation of sedimentary stratum thickness, inherited distortion or even abrupt change of stratum occurrence, zonation of plane fault combination and the variation of oil-water system in the same structure with no-lithologic change are the important signs for identifying subtle faults in Bohai Sea. The subtle faults greatly enlarge the size of the structural trap groups, and areas with dense subtle faults are often active area of hydrocarbon migration and accumulation and favorable exploration zones, which have strong control on the hydrocarbon accumulation. The identification method for subtle faults has guided the exploration in the mature areas of Bohai Sea effectively, with a number of large and medium oil and gas fields discovered, such as Bozhong 29-6 and Penglai 20-2.