The Longmen-Shan fault zone, at the eastern margin of the Tibetan Plateau, is one of the most extensively studied areas in the world, yet the deformation model and earthquake-generating mechanism remain subjects of vigorous debate. This paper presents a new three-dimensional (3-D) velocity model determined using a large volume of seismic data and two-dimensional (2-D) magnetotelluric (MT) profiles from previous studies, to investigate the mechanisms of crustal deformation and earthquake generation along the reverse-thrust and strike-slip fault zone. It has been observed that low-velocity, and low-resistivity anomalies related to the Sichuan foreland basin, is in sharp contrast to high-velocity and high-resistivity anomalies in the Songpan-Ganze block in the upper crust. The tomographic model presented here reveals two crustal bodies with low-velocity and high-conductivity anomalies underneath the Longmen-Shan fault zone, separated into three contrasting segments by the two crustal bodies. The two low-velocity and low-resistivity bodies have been interpreted as being associated with extrusion of either fluids or products of partial melting from the lower crust and/or the upper mantle. This suggests strong variations in the rheological strength of the rock along the fault zone. This finding implies that coupling between these presumably fluid-bearing bodies and earthquake generation could be extremely complex and that there is dramatic variation from the southwestern area to the northeastern segment along the fault belt. It is suggested here that this complex and variable deformation system along the fault zone played a principal role in controlling seismic generation and rupturing during the 2008 Wenchuan earthquake (Ms 8.0) and that it will do so again during possible future earthquakes in the region.