We have analyzed the thermochemical structure of the mantle in Central Europe, a complex area with a highly heterogeneous lithospheric structure reflecting the interplay of contraction, strike slip, subduction, and extension tectonics. Our modeling is based on an integrative 3‐D approach (LitMod) that combines in a self‐consistent manner concepts and data from thermodynamics, mineral physics, geochemistry, petrology, and solid Earth geophysics. This approach minimizes uncertainties of the estimates derived from modeling of various data sets separately. To further constrain our 3‐D model we have made use of the vast geophysical and geological data (2‐D and 3‐D, shallow/crustal versus deep lithospheric experiments) based on experiments performed in Central Europe in the past decades. Given the amount and the different nature/resolution of the available constraints, one of the most challenging tasks of this study was to consistently combine them, finding a trade‐off between all local and regional data sets available in a way that (i) preserves as many structural details as possible and (ii) summarizes those data sets into a single robust regional model. The resulting P/T‐dependent mantle densities are in LitMod 3‐D calculated based on a given mineralogical composition. They therefore provide more reliable estimates compared to pure gravity models, which enhance modeling of the crustal structures. Our results clearly indicate presence of several lithospheric domains characterized by distinct features, Pannonian Basin being one of the most outstanding ones. It has the thinnest crust and lithosphere in the area modeled, characterized by relatively fertile composition.