The deep structure of the Bohemian Massif (BM), the largest stable outcrop of Variscan rocks in central Europe, was studied using the data of the international seismic refraction experiment Central European Lithospheric Experiment Based on Refraction (CELEBRATION) 2000. The data were interpreted by seismic tomographic inversion and by two‐dimensional (2‐D) trial‐and‐error forward modeling of P and S waves. Additional constraint on crustal structure was given by amplitude modeling using the reflectivity method and gravity modeling. Though consolidated, the BM can be subdivided into several tectonic units separated by faults, shear zones, or thrusts reflecting varying influence of the Cadomian and Variscan orogeneses: the Saxothuringian, Barrandian, Moldanubian, and Moravian. Velocity models determine three types of crust‐mantle transition in the BM reflecting variable crustal thickness and delimiting contacts of tectonic units in depth. The NW area, the Saxothuringian, has a highly reflective lower crustal layer above Moho with a strong velocity contrast at the top of this layer. This reflective laminated lower crust reaches depths of 26–35 km and is characteristic for the Saxothuringian unit, which was subject to eastward subduction. The Moldanubian in the central part is characterized by the deepest (39 km) and the most pronounced Moho within the whole BM with a strong velocity contrast 6.9–8.1 km s−1. A thick crust‐mantle transition zone in the SE, with velocity increase from 6.8 to 7.8 km s−1 over the depth range of 23–40 km, seems to be the characteristic feature of the Moravian overthrusted by the Moldanubian during Variscan collision.