The Qieganbulake deposit associated with a mafic–ultramafic–carbonatite complex in the Kuluketage block is not only the world’s second-largest vermiculite deposit, but also a medium-size carbonatite-related phosphate deposit. Field observations, radiometric dating results and Sr–Nd–Hf isotopes reveal that the parental magmas of the carbonatite and mafic–ultramafic rocks are cogenetic and formed synchronously at c. 810 Ma. Geochemical characteristics and Sr–Nd–Hf–S isotopes ((87Sr/86Sr)i = 0.70581–0.70710; ϵNd(t) = −0.20 to −11.80; ϵHf(t) = −7.5 to −10.3; δ34S = +0.7 ‰ to +3.0 ‰ (some sulfides with high δ34S values (+3.2 to +6.6) were formed by late hydrothermal sulfur)), in combination with mineral compositions and previous research, strongly indicate that the Qieganbulake mafic–ultramafic–carbonatite complex formed via extensive crystal fractionation/cumulation and liquid immiscibility of a carbonated tholeiitic magma, possibly derived from partial melting of an enriched subcontinental lithospheric mantle previously modified by slab-released fluids and sediment input in a continental rift setting. The coupled enriched Sr–Nd isotopic signatures, in combination with previous research, suggest that the enriched subcontinental lithospheric mantle could have been metasomatized by asthenospheric mantle melts to different degrees. The Qieganbulake carbonatite-related phosphate ores were the products of normal fractional crystallization/cumulation of P–Fe3+ complex enriched carbonatite magma in high oxygen fugacity conditions, which was generated by liquid immiscibility of CO2–Fe–Ti–P-rich residual magma undergoing high differentiation.