The exact geological processes involved in the formation of subduction zone-related carbonatites remain ambiguous, along with their implications for crustal/carbon recycling in carbonatite melt generation. This study provides new geochemical and stable (C, O) and radiogenic (Sr, Nd, Pb) isotope data for Huangshuian carbonatite, located within the Lesser Qinling Orogen, with the aim to decipher its complex petrogenetic history. The carbonatites display elevated CaO, low MgO and alkali contents, and significant enrichments of Pb, Mo, and HREEs compared to typical carbonatites. The δ13CPDB (−4.6 to −4.9‰) and δ18OSMOW (+6.6 to +7.8‰) values plot within the field of primary igneous carbonatites. The carbonatites are characterized by consistent radiogenic isotopic compositions [(87Sr/86Sr)i = 0.70599–0.70603; εNd = −10.4 to −12.8; 206Pb/204Pb =16.24–17.74]. These combined results suggest that the carbonatites represent late-stage differentiation products of a parental, mantle-derived carbonatite melt. Their corresponding Sr-Nd-Pb isotopic compositions support the hypothesis that the Lesser Qinling carbonatites originate from a heterogeneous upper mantle source involving an EMI-like mantle component coupled with minor assimilation of the basement rocks. The parental carbonatite melt was derived by the melting of carbonate-bearing subcontinental lithospheric mantle metasomatized as the result of Early Triassic subduction of the Mianlue Ocean.