We present new crustal models of azimuthally anisotropic P-wave velocity, isotropic P-wave velocity (Vp), isotropic S-wave velocity (Vs) and Vp/Vs ratio for the Salton Trough. High Vp/Vs ratio is revealed at depths of 2–8 km along the San Andreas Fault, implying the possible presence of fluids. High Vp and high Vp/Vs ratio (>1.8) structures of the mid-lower crust beneath the Salton Trough possibly reflect the underplated gabbroic rocks as a result of the extension-induced partial melting of the upwelling asthenospheric materials. The fast velocity directions (FVDs) generally correlate with the direction of the maximum horizontal compressive stress except that fault-parallel FVDs are found at main fault traces. However, the FVDs in the Salton Trough show complex features. The northern Slaton Trough basin (the northern Salton Sea basin and Coachella Valley basin) is dominated by NW-SE FVDs, which are possibly due to the active compression happening there. E-W oriented FVDs predominate the upper crust of the southern Salton Trough basin (the southern Salton Sea basin and Imperial Valley basin), possibly due to faulting and/or block rotation. As the depth increases (12–18 km), the FVDs to the south of the Salton Sea have an overall rotation and gradually become NW-SE. The depth-dependent variation of anisotropy orientation may be attributed to a large band of underlying heat source that probably causes a change of stress field by imposing thermal stress on overlying rocks. In all, our velocity models suggest that faults in the Salton Trough may bear a high risk of mechanical failures due to the complexities of stress distribution and geological structures as well as the presence of a large volume of fluids and heat.