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The Carpathian–Pannonian Region (CPR) is one of the most seismically active areas in Central Europe, as evidenced by destructive events such as the Mw 7.7 Vrancea earthquake of 1940. Understanding the crustal structure beneath the CPR is essential for understanding earthquake processes, improving high-resolution earthquake location, and mitigating seismic hazard. In this study, we present a 3-D S-wave velocity model of the CPR obtained by jointly inverting group and phase velocity dispersion data using a trans-dimensional Bayesian approach. This method provides a more robust, well-resolved crustal and uppermost-mantle structure than previous studies relying solely on group-velocity inversion. Our results show low velocities at 5–10 km depth beneath the Pannonian Basin, and elevated velocities at ~30 km depth beneath the Great Hungarian Plain, while surrounding mountain regions exhibit relatively low velocities at ~40 km depth. Velocities become nearly uniform by a depth of 50 km. Cross-sections reveal a pronounced upper-crustal low-velocity zone beneath the basin and a mid-crustal low-velocity layer at ~20 km depth along the Tisza–Dacia profile, producing a layered geometry resembling the “crocodile” pattern reported in other tectonically complex regions. Importantly, the Moho is expressed at different S-wave velocity levels across the CPR: the 3.8 km/s isoline is close to the Moho beneath the basin, whereas the 4.2 km/s isoline better represents the deeper Moho beneath the surrounding mountains reported by previous studies (Thapa & Vlahovic, 2025). Identifying the Moho using region-appropriate Vs iso-velocity values highlights how variations in crustal composition and thermal structure influence the Moho’s seismic velocity signature. Our study provides a refined crustal framework of the CPR, providing critical constraints for understanding its tectonic evolution and improving regional seismic hazard assessment.