We calculate the depth to magnetic basement and the average crustal magnetic susceptibility, which is sensitive to the presence of iron-rich minerals, to interpret the present structure and the tecto-magmatic evolution in the Central Tethyan belt. Our results demonstrate exceptional variability of crustal magnetization with smooth, small-amplitude anomalies in the Gondwana realm and short-wavelength high-amplitude variations in the Laurentia realm. Poor correlation between known ophiolites and magnetization anomalies indicates that Tethyan ophiolites are relatively poorly magnetized, which we explain by demagnetization during recent magmatism. We analyze regional magnetic characteristics for mapping previously unknown oceanic fragments and mafic intrusions, hidden beneath sedimentary sequences or overprinted by tectono-magmatic events. By the style of crustal magnetization, we distinguish three types of basins and demonstrate that many small-size basins host large volumes of magmatic rocks within or below the sedimentary cover. We map the width of magmatic arcs to estimate paleo-subduction dip angle and find no systematic variation between the Neo-Tethys and Paleo-Tethys subduction systems, while the Pontides magmatic arc has shallow (∼15°) dip in the east and steep (∼50°–55°) dip in the west. We recognize an unknown, buried 450 km-long magmatic arc along the western margin of the Kırşehir massif formed above steep (55°) subduction. We propose that lithosphere fragmentation associated with Neo-Tethys subduction systems may explain high-amplitude, high-gradient crustal magnetization in the Caucasus Large Igneous Province. Our results challenge conventional regional geological models, such as Neo-Tethyan subduction below the Greater Caucasus, and call for reevaluation of the regional paleotectonics.