The Kalguty Mo–W ore-magmatic system (OMS) is a granite batholith (S = 70 km2, V = 12,800 km3 at the recent denudation level, according to geological and geophysical data). This batholith is cut by the East Kalguty belt of rare-metal ongonite–elvan dikes spatially and temporally associated with the East Kalguty quartz-vein–greisen Mo–W deposit. Geological and petrogenetic studies along with published and our new results of geochronological (U/Pb zircon, Re/Os molybdenite, and 40Ar/39Ar biotite and muscovite) dating made it possible to reconstruct the thermochronological history of the Kalguty OMS. Five stages have been recognized: I (215 ± 1 Ma)—formation of granites of major intrusive phase and of Mo-rich mineralization, which is an orebody called the Molybdenum stock; II (206 ± 1 Ma)—formation of leucogranite and intragranitic-pegmatite stocks in the granites of major intrusive phase; III (202 ± 1 Ma)—formation of most of ongonite–elvan dikes composing a dike belt; IV (195 ± 1 Ma)—formation of long ultrarare-metal ongonite–elvan dikes in the central part of the dike belt, which is spatially associated with the W-rich veins of the deposit; and V (181 ± 1 Ma)—formation of thin ongonite–elvan dikes on the periphery of the dike belt. The recognized age stages of the Kalguty Mo–W ore-magmatic system were mathematically tested based on the model of crystallization differentiation and the dynamics of heat and mass transfer in the magma chamber corresponding to the Kalguty granite batholith. The results obtained show that the formation of a granite batholith (215 ± 1 Ma) and a later ongonite–elvan dike complex with Mo–W-rich mineralization (195 ± 1 Ma) can be explained only by a two-level ore-magmatic system with the “upper” granite batholith at a depth of 5–15 km and the “lower” granite chamber at a depth of 20–31 km. The total duration of ore-magmatic processes is 20 Myr (ore production stage) or 30 Myr, if we take into account occasional elvan dikes with poor quartz–fluorite–barite–ferberite mineralization (181 ± 1 Ma) on the periphery of the Kalguty deposit.