The Teisseyre-Tornquist Zone (TTZ) is the longest pre-Alpine tectonic lineament in Europe. Its nature and structural evolution are controversially debated. In this study, we show its structural evolution beneath the southern Baltic Sea both on crustal and basin scale by using three seismic reflection profiles combined with 2-D potential field data. The results demonstrate that the southern Baltic Sea is underlain by a thick crust of the East European Craton (EEC) with a Moho depth in the range of 38-42 km. The overall crustal architecture is shaped by three phases of localized crustal stretching in early Paleozoic, Devonian-Carboniferous, and Permian-Mesozoic. The most spectacular feature of the southern Baltic Sea are zones of thick-skinned compressional deformation produced by Alpine inversion along the TTZ and Sorgenfrei-Tornquist Zone (STZ). Both zones include a system of thrusts and back thrusts penetrating the entire crust in an 80-90 km wide inversion zone superimposed on the EEC crust and its sedimentary cover. ENE-vergent thrusts are traced from the top of the Cretaceous down to the Moho and they are accompanied by back thrusts of opposite vergence, also reaching the Moho. Inversion tectonics resulted in the uplift of a block of cratonic crust as a pop-up structure, bounded by thrusts and back thrusts, and the displacement of the Moho within the STZ and TTZ. The similar mechanism of intra-cratonic inversion was recognized for the Dnieper-Donbas Basin in Ukraine, and it may be characteristic of rigid cratons, where deformation is localized in a few preexisting zones of weakness.