We present the first thermal model for the lithosphere in Turkey, which shows a highly heterogeneous pattern associated with mosaics of the Tethyan and modern subduction systems. We calculate a regionally average crustal density of 2.90 g/cm3 consistent with the presence of large volumes of mafic material. The Moho temperature with a regionally average value of 650–850 °C shows strong short‐wavelength variations. Lithosphere thinning to 50–75 km in most of western Anatolia may have developed in response to the Hellenic slab rollback, while the Neoproterozoic block in the Menderes Massif preserves a 150 km deep lithosphere root. In central Anatolia, the lithosphere thickness decreases southward from 100–150 to 50–60 km along a linear belt of young basaltic volcanism, followed by a belt of a 150 km thick lithosphere. We interpret this characteristic pattern by a SE dipping paleoslab beneath the western Taurides, which may cause the Cyprus subduction melting zone to deviate toward NW and NE. The Eastern Pontides‐Lesser Caucasus have 150–200 km thick lithosphere roots caused by collisional tectonics. The East Anatolian Plateau is underlain by a 80–140 km thick lithosphere, which suggests the presence of significant continental fragments; the patchy pattern of its thermal heterogeneity may be explained by teared and fragmented Tethyan slabs. A poor correlation between the lithosphere thermal structure, heat flux, the Neogene volcanic regions, and mantle seismic velocities implies that seismic anomalies are essentially controlled by heterogeneous mantle hydration by subduction systems of different ages and cannot be explained by temperature variations alone.