Two intrusive complexes are recognized at the Shakhtama deposit: Shakhtama and ore-bearing porphyry. The U–Pb zircon dates (SHRIMP II) are 161.7 ± 1.4 and 161.0 ± 1.7 Ma for the monzonites and granites of the Shakhtama complex and 159.3 ± 0.9 and 155.0 ± 1.7 Ma for the monzonite- and granite-porphyry of the ore-bearing complex. The igneous complexes formed in a complex geodynamic setting in the late Middle Jurassic and early Late Jurassic, respectively. The setting combined the collision of continents during the closure of the Mongol-Okhotsk ocean and the influence of mantle plume on the lithosphere of the Central Asian orogenic belt. The intrusion of the Shakhtama granitoids took place at the end of the collision, and the intrusion of porphyry of the ore-bearing complex, during the change of the geodynamic setting by a postcollisional (rifting) one. The complexes are composed of monzonite–granite series with similar geochemical characteristics of rocks. The performed geological, geochemical, and isotope-geochemical studies suggest that the sources of magmas were juvenile crust and Precambrian metaintrusive bodies. The juvenile mafic crust is considered to be the predominant source of fluid components and metals of the Shakhtama ore-magmatic system. The granitoids of both complexes include calc-alkalic high-K rocks with typical geochemical characteristics and with characteristics of K-adakites. These geochemical features indicate that the parental melts of the former rocks were generated at depths shallower than 55 km, and the melts of the latter, at depths of 55–66 km. K-adakite melts resulted from the melting of crust submerged into the mantle during the lithosphere delamination, which was caused by the crust thickening as a result of the repeated inflow of basic magma into the basement of the crust and tectonic deformations in its upper horizons. The high-Mg monzonitic magma produced under these conditions ascended and was mixed with melts generated in the upper horizons, which accounts for the high Mg contents of the Shakhtama granitoids. The similar compositions and petrogeochemical characteristics of the granitoids of the Shakhtama and porphyry complexes point to the same sources, transport paths, and evolution trend of their parental melts. This indicates that the igneous rocks of both complexes are products of the same long-living magmatic system, which produced Mo mineralization at the final stage. The favorable conditions for the ore production in the magmatic system during the formation of the porphyry complex appeared as early as the preceding stage—during the formation of the Shakhtama complex, which we regard as a preparatory stage in the evolution of the ore-magmatic system.