The study addresses the space distribution of lithospheric density contrasts in 3D and 2D surface (spherical) sources of gravity anomalies to depths of 120 km below the geoid surface and their relationship with shallow deformation and Archean, Early Paleozoic, and Late Mesozoic geodynamic environments. The lithospheric section in northeastern Transbaikalia and the Upper Amur region includes two layers of low-density gradients attendant with low seismic velocities and low electrical resistivity. The lower layer at depths of 80–120 km is attributed to an asthenospheric upwarp that extends beneath the North Asian craton from the Emuershan volcanic belt and the Songliao basin. The concentric pattern of density contrasts in the middle and lower crust beneath the Upper Amur region may be produced by the activity of the Aldan-Zeya plume, which spatially correlates with the geometry of the asthenospheric upwarp as well as with the regional seismicity field, magnetic and heat flow anomalies, and stresses caused by large earthquakes and recent vertical crustal movements. The relationship between shallow and deep structures in the crust and upper mantle bears signature of horizontal displacement (subduction) of the lower crust of the Baikal-Vitim and Amur superterranes beneath the North Asian craton.