We interpret seven two-dimensional deep-penetration and long-offset multi-channel seismic profiles in the northernmost South China Sea area, which were collected by R/V Marcus G. Langseth during the TAIwan GEodynamics Research (TAIGER) project in 2009. To constrain the crustal characteristics, magnetic inversion and forward magnetic modeling were also performed. The seismic results clearly show tilted faulting blocks in the upper crust and most of the fault plane connects downward to a quasi-horizontal detachment as its bottom in the south of the Luzon-Ryukyu transform plate boundary. North of the plate boundary, a small-scale failed rifted basin (minimum 5 km in crustal thickness) with negative magnetization probably indicates an extended continental origin. Significant lower crustal material (LCM) was imaged under a crustal fracture area which indicated a continent and ocean transition origin. The thickest LCM (up to 6. 5 km) is located at magnetic isochron C15 that is probably caused by the magma supply composite of a Miocene syn-rift volcanic event and Pliocene Dongsha volcanic activity for submarine volcanoes and sills in the surrounding area. The LCM also caused Miocene crustal blocks to be uplifted reversely as 17 km crustal thickness especially in the area of magnetic isochron C15 and C16. In addition, the wide fault blocks and LCM co-existed on the magnetic striped area (i. e. C15-C17) in the south of the Luzon-Ryukyu transform plate boundary. Magnetic forward modeling suggests that the whole thick crustal thickness (>12 km thick) needs to be magnetized in striped way as oceanic crust. However, the result also shows that the misfit between observed and synthetic magnetic anomaly is about 40 nT, north of isochron C16. The interval velocity derived from pre-stack time migration suggests that the crust is composed of basaltic intrusive upper crust and lower crustal material. The crustal nature should refer to a transition between continent and ocean. Thus, the magnetic reversals may be produced in two possible ways: basaltic magma injected along the crustal weak zone across magnetic reversal epoch and because some undiscovered ancient piece of oceanic crust existed. The crustal structure discrimination still needs to be confirmed by future studies.