The Mushgai-Khudag alkaline‑carbonatite complex, located in southern Mongolia within the Central Asian Orogenic Belt (CAOB), comprises a broad range of volcanic and subvolcanic alkaline silicate rocks (melanephelinite-trachyte and shonkinite-alkaline syenite, respectively). Magnetite-apatite rocks, carbonatites, and fluorite mineralization are also manifested in this area. The complex formed between 145 and 133 Ma and is contemporaneous with late Mesozoic alkaline–carbonatite magmatism within the CAOB. Major and trace element characteristics of silicate rocks in the Mushgai-Khudag complex imply that these rocks were formed by the fractional crystallization of alkaline ultramafic parental magma. Magnetite-apatite rocks may be a product of silicate-Ca-Fe-P liquid immiscibility that took place during the alkaline syenite crystallization stage. The Mushgai-Khudag rocks have variable and moderately radiogenic Sr (87Sr/86Sr(i) = 0.70532–0.70614), ƐNd(t) = −1.23 to 1.25) isotopic compositions. LILE/HFSE values and Sr[sbnd]Nd isotope compositions indicate that the parental melts of Mushgai-Khudag were derived from a lithospheric mantle source that was affected by a metasomatic agent in the form a mixture of subducted oceanic crust and its sedimentary components. The δ18OSMOW and δ18CPDB values for calcites in carbonatites range from 16.8‰ to 19.2‰ and from −3.9‰ to 2.0‰, respectively. C[sbnd]O covariations in calcites of the Mushgai-Khudag carbonatites can be explained by the slight host limestone assimilation.