The subsidence history and sedimentary architecture of extensional basins are controlled by the interplay between tectonics, mantle dynamics, and climatic variations. Observations from outcrop to regional seismic scales coupled with numerical modelling techniques, including basin-scale stratigraphic, crustal-scale tectonic and mantle-scale subduction models contribute to quantify basin evolution. Here, we review and discuss both tectonic and stratigraphic applications of such models and compare them with observations from the Pannonian Basin system of Central Europe. We show that diachronous localization of back-arc extension, crustal thinning, asthenospheric upwelling and subsequent thermal relaxation are superimposed on an overall slow plate convergence. These processes result in contrasting subsidence and uplift patterns and a variable heat flow evolution in different parts of the basin system. The crustal stress-field of the subbasins does not always reflect their contrasting vertical motions. Extensional deformation generally migrates from the basin margins towards the basin centre. Structural inversion is localized along hot and weak inherited zones from the Middle Miocene to Present. Tectonic subsidence focuses sedimentation along deep depocenters, sourced by exhumed footwalls and from the neighbouring orogens. The overall post-rift sediment progradation are influenced by inherited bathymetries from the preceding syn-rift stage and by enhanced differential vertical motions.