Using arrival time data, we determined seismic structure of the Longmen Shan by S-wave tomography and studied its relations with the Ms 8.0 earthquake in Wenchuan, southwestern China. Our results suggest that the Longmen Shan fault belt is a rheologic boundary between the eastern Tibetan plateau and the Sichuan basin, and the deep crust of the entire Longmen Shan is significantly thickened by ductile deformation. The upper structure of the eastern Tibetan plateau is cored by the high-velocity Pengguan massif. Its collision with the Sichuan basin is the most direct reason for the seismic ruptures on the Longmen Shan fault belt north of Wenchuan, while the lack of earthquakes south of Wenchuan is related to the weakness of the crust. Therefore, The Ms 8.0 earthquake occurred in a strongly heterogeneous region. The variations in the crustal structure largely controlled the initial rupture of the Ms 8.0 earthquake and aftershock activity.