The northern South China Sea (SCS) plate between Taiwan and the Philippines experienced complex underplating and overriding. Ocean-bottom seismometer (OBS) data along the southern profile (20.5 °N) with 18 OBSs, the NE-SW profile with 11 OBSs and the northern profile (21.5 °N) with 12 OBSs were collected from a large-offset active-source seismic survey during the 2009 Taiwan Integrated Geodynamics Research. Here we re-analyzed the OBS data to image the transitional continental crust (TCC) and the subducted slab across the northern SCS, the Manila Trench, the deformation front (DF) and the accretionary wedge off southwestern Taiwan. By picking both refracted and reflected arrivals from OBS data and adopting irregular grids during modeling, we have derived P-wave velocities and interfaces of the crustal structures to identify the characteristics of the crustal structures and the collision-subduction transitional zone in the northern SCS. Based on the lateral velocity variation (2.5–5 km/s) of the accretionary wedge along three OBS profiles, the geometry of the splay faults on top of a décollement was imaged. Brittle deformation due to the hardened sediment with a relatively high velocity (3.5–5.5 km/s) from the collision was also found between a mid-crust detachment and the décollement along the NE-SW profile. Our study indicates the deeper Moho in the south (15–18 km deep) but shallower in the north (14–17 km deep), and the Moho is generally shallower than that derived from the previous studies. West of the trench or the DF, the TCC in the northern SCS has been identified in shallow crustal layers while underplated by the thick oceanic crust or the oceanic crust from the SCS in the middle and lower crustal layers. East of the trench or the DF, the TCC in the upper and middle crust has subducted beneath the accretionary wedge. We found a failed rift zone west of the DF along the northern profile. One seismically active region with large lateral velocity change (2.5–4.5 km/s) in the accretionary wedge was imaged. Another seismically active region is near the southern end of the Kaoping Canyon where the crustal thickness from the basement to the Moho is extremely thin (8 km).