Using earthquake data from the Sichuan seismic network, the S-wave velocity structure of the Longmen Shan area was reconstructed by a body wave seismic tomography. It is followed by an analysis of the crustal structure along the Longmen Shan fault zone and in the Wenchuan earthquake area. Seismic rupture is well correlated with the Longmen Shan fault zone and the variation of crustal structure on the east and west of the fault zone. On the north of Wenchuan, the upper crust of the Longmen Shan has relatively high strength and is uplifted apparently. The Pengguan massif between Guanxian and Jiangyou is the main area for stress accumulation on the west of the Longmen Shan. The Wenchuan earthquake is located on the southern edge of this area. The rigid basement of the crust of the Sichuan basin underthrusts beneath the Longmen Shan, and the Wenchuan earthquake can be attributed to the collision of its western bulge with the base of the Pengguan massif along the Longmen Shan fault zone near Wenchuan. On the contrary, the Longmen Shan south of Wenchuan has a weak upper crust with lower mechanical strength, where stress is not easy to accumulate, compared with the northern Longmen Shan. It partly explains a lack of aftershocks along the Longmen Shan fault zone south of Wenchuan. Crustal thickening is observed beneath the Longmen Shan and this is because the strong lithosphere of the Sichuan basin obstructs the eastward flow of the weak crust of the eastern Tibetan. A large part of shortening is accommodated in a manner of ductile deformation, which causes the thickening of the deep crust and the downward flex of the Moho, while the upper crust is uplifted and folded, forming high mountains in the Longmen Shan.