New structural and petrological data have been obtained for the zone of Siberia-Kazakhstan oblique collision for Permian time. In terms of classical tectonics, the area coincides with the Zaisan folded area produced by closure of the Char paleo-ocean in the Late Carboniferous. However, the extent, structure, and composition of magmatism at the Carboniferous-Permian (280±10 Ma) and Permian-Triassic (250±5 Ma) boundaries require an active control from Morgan-type lower mantle plumes (Tarim and Siberian plumes). Structure formation in the lithosphere and heat sources of magmatism have been simulated in a 3D model including lithospheric strain rates (with regard to viscosity layering) and subcontinental upper mantle convection. According to our model, heat supply from slab break-off and/or delamination of lithosphere is insufficient to maintain large-scale mantle-crustal magmatism in the case of oblique collision between 80–100 km thick plates (“soft collision”). The Late Paleozoic-Early Mesozoic Altai is considered as a model of a large hot shear zone, a particular structure produced by interference of plate- and plume-tectonic processes. Special attention is given to structural and petrological markers of plume tectonics (reported for the case of the Altai collisional shear system), with their diagnostic features useful for understanding geodynamics of other similar regions.