Modeling of the seismic, thermal, and density structure of the Siberian craton lithospheric mantle at depths of 100–300 km has been performed along the superlong Meteorite and Rift seismic profiles. The 2D velocity sections reflect the specific features of the internal structure of the craton: lateral inhomogeneities, seismic-boundary relief at depths of ~ 100, 150, 240, and 300 km, velocities of 8.3-8.7 km/s, and the lack of low-velocity zone in the lower lithosphere. Mapping of the thermal state along the Meteorite and Rift profiles shows a significant temperature decrease in the cratonic mantle as compared with the average temperatures of the surrounding Phanerozoic mantle (> 300 °C) estimated from the global reference model AK135. Lateral temperature variations, reflecting the thermal anomalies in the cratonic keel, are observed at depths of < 200 km (with some decrease in temperature in the central part of the craton), whereas at depths of > 200 km, temperature variations are negligible. This suggests the preservation of residual thermal perturbations at the base of the lithosphere, which must lead to the temperature equalization in the transition zone between the lithosphere and the asthenosphere. Variations in chemical composition have a negligible effect on the thermal state but affect strongly the density structure of the mantle. The results of modeling admit a significant fertilization of matter at depths more than 180–200 km and stratification of the cratonic mantle by chemical composition. The thicknesses of chemical (petrologic) and thermal boundary layers beneath the Siberian craton are estimated. The petrologic lithosphere is localized at depths of ~ 200 km. The bottom of the thermal boundary layer is close to the 1450 °C isotherm and is localized at a depth of 300 km, which agrees with heat flow and seismic-tomography data.