During the CELEBRATION 2000 seismic experiment, the Western Carpathians and Pannonian basin region was investigated by a dense system of deep seismic sounding profiles. In this paper, we present the results of modeling refracted and reflected waves employing 2D ray tracing for seven interlocking profiles that were jointly modeled and interpreted with the constraint that the models match at the crossing points of the profiles. The resulting P-wave velocity models reveal complex structures in the crust and large variations in the depth of the Moho discontinuity (∼25–45 km). In the southern part of the area, the relatively thin Pannonian basin crust consists of 3–7 km thick sediments and two crustal layers with velocities of 5.9–6.3 km/s in the upper crust and 6.3–6.6 km/s in the lower crust. In the central region, the upper crust of the ALCAPA (Alpine–Carpathian–Pannonian) microplate contains a high velocity body of Vp ≥ 6.4 km/s, which spatially corresponds with the Bükk Composite Terrane. The total thickness of the ALCAPA crust is 1-2 km greater than in the adjacent Tisza–Dacia microplate. To the north in the area of the Trans-European suture zone (TESZ) and Carpathian foredeep, we observe a 10–20 km thick upper crust with low velocity (Vp ≤ 6.0 km/s). Sub-Moho velocities have average values of 7.8–8.0 km/s for the Pannonian basin, while in the Western Carpathians, the TESZ and the East European Craton (EEC) area, they are slightly higher (8.0–8.1 km/s). Lower velocities beneath the ALCAPA and Tisza–Dacia microplates could be caused by compositional variations and the significantly higher surface heat flow. Beneath some profiles, reflectors in the lithospheric mantle were found sub-parallel to the Moho but 10–20 km below it. Our integrated geophysical and geological analysis indicates that the observed structure was created by collision of two lithospheric plates with only a moderate degree of convergence. The northern plate consists of older European tectonic units of the EEC and TESZ. However, the southern one consists of younger tectonic units of the Western Carpathians and the back-arc Pannonian basin that generated the ALCAPA and Tisza–Dacia microplates. We interpret the complex present day structure to be the result of the soft continental collision between the ALCAPA and Tisza–Dacia microplates and the south margin of the European plate, which was mainly followed by the extensional process beneath the back-arc Pannonian basin.