We modeled crustal and lithospheric thickness variation as well as the variations in temperature, composition, S wave seismic velocity, and density of the lithosphere beneath the Saharan Metacraton (SMC) applying an interdisciplinary 3‐D modeling. Regardless of the limited data set, we aimed at consistent imaging of the SMC lithospheric structure by combining independent data sets to better understand the evolution of the metacraton. We considered that the SMC was once an intact Archean‐Paleoproterozoic craton but was metacratonized during the Neoproterozoic due to partial loss of its subcontinental lithospheric mantle (SCLM) during collisional processes along its margin. This has permitted the preservation of three cratonic remnants (Murzuq, Al‐Kufrah, and Chad) within the metacraton. These cratonic remnants are overlain by Paleozoic‐Mesozoic sedimentary basins (Murzuq, Al‐Kufrah, and Chad), which are separated by topographic swells associated with the Hoggar Swell, Tibesti Massif, and Darfur Dome Cenozoic volcanism. The three cratonic remnants are underlain by a relatively thicker lithosphere compared to the surrounding SMC, with the thickest located beneath Al‐Kufrah reaching 200 km. Also, the SCLM beneath Al‐Kufrah cratonic remnant is significantly colder and denser. Modeling of the lithosphere beneath the Chad and Murzuq Basins yielded a complex density and temperature distribution pattern, with lower values than beneath the Tibesti Massif. Further, our modeling indicated a uniform and moderately depleted mantle composition beneath the SMC. The presence of a relatively thinner lithosphere beneath the noncratonic regions of the SMC is attributed with several tectonic events, including partial SCLM delamination during the Neoproterozoic, Mesozoic‐Cenozoic rifting, and Cenozoic volcanism.