The structural setting and deformation history are very important aspects of understanding the frequent earthquakes and assessing the hazards. In this paper, we interpret two new seismic profiles that were collected after the Wenchuan Mw7.9 earthquakes occurred on May, 2008. Our interpretation has integrated four wells, three seismic profiles and the surface geology to reveal structural characteristics of the central Longmen Shan thrust. The drilled wells reveal that there are two detachments within the upper Triassic and the lower Triassic at the Longmen Shan thrusts. The shallow detachment fault transferred its slip to the basin and made another deformation inner the Sichuan basin. Between the shallow detachments, many faults developed and the major structures at the thrust front have formed as structural wedges. Both the drilled wells and seismic interpretation show the upper Triassic repeated in the depth. The shortening at the central Longmen Shan thrust is approximately 30%–37%. According to geological survey and the seismic interpretation, the foreland basin was developed during the late Triassic and the angular unconformity between the lower Jurassic and the upper Triassic at the Longmen Shan front. Several different tectonic events can be identified since the Mesozoic, which indicated that the Longmen Shan has a complex evolution history. In our model, the major Beichuan fault (F2) and the Pengguan fault (F3) at the central Longmen Shan dip steeply near the surface but are more gentle-dipping at depth. Both of the shallow thrusting and the basement shortening made contribution to the rapid uplift of the Longmen Shan during the Cenozoic. The co-seismic ruptured fault is like a branchy fault that developed on the major fault system. The Wenchuan Mw7.9 earthquake and the Lushan Mw6.7 earthquake may be related to the reaction of the basement structures.