The Manila subduction zone is the eastern boundary of the South China Sea (SCS) which records key information on the evolution of the SCS, also is an area with active earthquakes and tsunamis. Using high resolution multi-channel seismic data across the northern Manila subduction zone, this paper characterizes the tectonic deformation and structure of the frontal accretionary wedge as well as magmatism and sedimentary features of the oceanic basin and trench in the subduction zone. Results show that the lower slope of accretionary wedge consists mainly of imbricated thrusts, structural wedges and blind thrusts that act as frontal faults, whereas the internal architecture of the upper slope is difficult to identify because of intense deformation and magmatism. All the thrust faults merged into a lower Miocene decollement which cuts off the middle Miocene strata and can be traced upward into the Pliocene strata, indicating that the fault is influenced by local buried seamounts and basement uplift below the accretionary wedge. Magmatic activities lasted from late Miocene to Quaternary in the oceanic basin, trench and accretionary wedge in the study area. We suggest that the accretionary wedge of the northern Manila subduction zone begun to thrust before 16. 5 Ma and is still propagating to the SCS through piggyback thrusting at present. The Manila subduction zone probably initiated in the late Oligocene when the oceanic basin of the SCS continued to spread. The region of hyper-extended continental crust extends from the continental slope to the oceanic basin between 19 degrees N and 21 degrees N in the northeastern SCS. The subduction of this hyper-extended continental crust resulted in a significant variation in the geometry of the northern Manila trench, which shows a concave eastward pattern to the Luzon Arc.