The Zagros fold-and-thrust belt is the principal response to the Arabia–Eurasia continental collision, which generates significant seismic activity in Iran. Surface wave tomography can be a proper tool for crustal structure imaging in this region. We used observed dispersion curves of Rayleigh wave derived from high-quality local-earthquake waveforms to obtain 2D tomographic maps in the period range 1–28 s beneath the Zagros collision zone. Subsequently, local pseudo-dispersion curves for individual grid points are inverted for shear-wave velocity structure, in order to obtain a 3D velocity model of the crust. Our results indicate shallow low-velocity structures near the suture zone. Moreover, a low-velocity flexure shape in the south of the Zagros Mountain Front Fault could be due to the thick sedimentary basin beneath the Dezful embayment. Relatively an uplifting of the deeper structures beneath Sanandaj-Sirjan and the high Zagros might could be led to high-velocity structures at mid-crustal depths. The variation of shear-wave velocity along the Zagros indicates the inhomogeneous structures along this folding and thrust belt.