The question of plate boundary forces and deep versus shallow asthenospheric uplift has long been debated in intracontinental rift areas, particularly in the Baikal rift zone, Asia, which is colder than other continental rifts. As previous gravity and teleseismic studies support the dominance of opposing mechanisms in the Baikal rift, we reconsidered both data sets and jointly inverted them. This more effective approach brings insight into location of the perturbing bodies related to the extension in this region. Our new joint inversion method allows for inverting the velocity‐density relationship with independent model parametrization. We obtain velocity and density models that consistently show (1) crustal heterogeneities that coincide with the main tectonic features at the surface, (2) a faster and denser cratonic mantle NW of Lake Baikal that we relate to the thermal contrast between old and depleted Archean (Siberian platform) and Paleozoic orogenic belt (Sayan‐Baikal belt), (3) three‐dimensional topographic variations of the crust‐mantle boundary with well‐located upwarpings, and (4) the lithosphere‐asthenosphere boundary uplift up to 70 km depth with a NW dip. Our resulting velocity and density models support the idea of a combined influence of lithospheric extension and inherited lithospheric heterogeneities for the origin of the Baikal rift zone.