The Sea of Marmara and its basins mainly evolved due to the activities of the Thrace-Eskisehir Fault Zone (TEFZ)in Neogene and the North Anatolian Fault Zone (NAFZ) in Quaternary. At present-day, the Sea of Marmara is stillevolving due to the NAFZ and the Marmara region is an earthquake danger zone while hosting around 20 million ofinhabitants. For a better understanding of the tectonic processes and geodynamic evolution, it is important to modelthe geological structure and the thermal field of this region. The aim of this study is to build a 3D lithospheric-scalestructural model and a 3D conductive thermal model for the Sea of Marmara and including its adjacent onshoreareas. Therefore, we integrate different geological and geophysical data such as existing structural models, welldata, seismic observations and gravity to build a new 3D lithospheric-scale structural model which is additionallyconstrained by 3D gravity modeling. The final 3D structural model differentiates various sedimentary, crustal andmantle units and is the base for the 3D thermal field calculation. The 3D conductive thermal model is a numerical solution to the Fourier’s law equation in steady-state condition and considering the thermal properties of thecorresponding structural model. Our 3D lithospheric-scale models of the geological structure and the conductivethermal field are the key points for further general research and useful particularly for mechanical modeling, considering variations in rheology and strength of the lithosphere in the Marmara region. In addition, our results haveapplication in geo-resources exploration and would be helpful in risk management and hazard mitigation.