Carbonatites with heavy rare earth element (HREE) enrichment are a rare and intriguing prospect for economic geology research, due to the growing global demand for HREEs in various industries. However, debate persists over the mechanism responsible for HREE enrichment in carbonatites, with the mantle source, magmatic-hydrothermal evolution, or a combination of these factors proposed to be responsible. This study examines three adjacent Late Triassic carbonatites (from the Huanglongpu, Huayangchuan, and Jialu carbonatite dike systems) in the Lesser Qinling of Central China and uses Mo isotope systematics to provide unique insights into the HREE enrichment process of these magmas. All three carbonatites exhibit elevated total REE (ΣREE) concentrations (up to 4600 ppm), along with significant HREE enrichment (ΣHREE/ΣREE = 0.1−0.4). Notably, Jialu carbonatite stands out for having the highest total HREE concentrations (≥360 ppm) and ΣHREE/ΣREE ratios (0.2−0.4). Regardless of their variable degrees of HREE enrichment, the three carbonatites display similar Sr-Nd-Pb isotope signatures, which indicates a shared enriched mantle source. The Huanglongpu and Huayangchuan carbonatites mostly display significantly lighter δ98/95Mo (−1.71‰ to −0.15‰) values than the depleted mantle, which indicates an origin from an enriched mantle influenced by recycled pelagic clays and Fe-Mn nodules. Both types of marine sediments are enriched in REEs and would have undergone initial HREE enrichment during slab dehydration and metamorphism, resulting in an HREE-enriched mantle source region. In contrast, Jialu carbonatite possesses significantly heavier δ98/95Mo (0.13‰−1.89‰), which is indicative of the subsequent influence of hydrothermal processes. Additional evidence of this hydrothermal influence at Jialu is preserved in calcite crystal fluid inclusions, elevated δ18O (8.71‰−10.72‰), non-charge-and-radius−controlled (CHARAC) Y/Ho ratios (36−41), and low Sr concentrations (<4800 ppm). Secondary upgrading of HREEs at Jialu occurred due to preferential complexation and transportation during hydrothermal exsolution. This study demonstrates that maximum HREE enrichment in carbonatites is achieved through a two-stage process that involves both a refertilized mantle source and late-stage hydrothermal exsolution.