In the Late Paleozoic–Early Mesozoic, the Central Asian Rift System formed in the southern framing of the Siberian Craton. It has a specific structure owing to zoned magmatic areas comprising the largest world’s batholiths (Angara–Vitim, Khangai, and Khentei) in the core and coeval rift zones on the periphery. By the example of the Khangai batholith, which is the core of the Khangai zoned magmatic area, we have demonstrated that the batholith granites are a specific class of anorogenic granitoids. Each batholith is composed of nearly coeval rocks of widely varying compositions, from low-alkali to subalkalic and alkaline and from mafic to ultrafelsic. The geochemical and isotopic characteristics of rocks of the Khangai batholith are intermediate between the host continental crust and the juvenile mantle source. The melts from this mantle source formed lava sequences on the rift periphery of the batholith and were also manifested in its core as synplutonic mafic intrusions. The isotope-geochemical characteristics of the batholith granitoids evidence that mantle magmas took part in the formation of granite melts. With regard to the volume of the batholith rocks (~1 mln km3), the Khangai zoned magmatic area can be considered a silicic large igneous province, whose formation was controlled by a localized source of material and heat, i.e., mantle plume. We propose a model relating the composition, structure, and geologic position of batholiths to the impact of mantle plumes on the lithosphere of a folded area. The model assumes that mantle melts intruded into the base of crust by the underplating mechanism or formed underlayers, caused crustal anatexis, and were mixed with anatectic melts. The geochemical and isotopic characteristics of the resulted magmatic products were intermediate between the parameters typical of the convergent boundaries of lithospheric plates and those characteristic for intraplate environments.