The Huayangchuan deposit in the North Qinling alkaline province of Central China is a unique carbonatite-hosted giant U–Nb–REE polymetallic deposit. The mineralization is characterized by the presence of betafite, monazite, and allanite as the main ore minerals, but also exhibit relatively high budgets of heavy rare earth elements (HREE = Gd–Lu and Y). The origin of carbonatites has long been controversial, thus hindering our understanding of the genesis of the deposit. Here, we conducted an in-situ trace elemental, Sr–Nd isotopic, and bulk C–O isotopic analyses of multi-type calcites in the deposit. Two principal types (Cal-I and Cal-II), including three sub-types (Cal-I-1, Cal-I-2 and Cal-I-3) of calcites were identified based on crosscutting relationships and calcite textures. Texturally, Cal-I calcites in carbonatites display cumulates with the grain size decreasing from early coarse- (Cal-I-1) to medium- (Cal-I-2) and late fine-grained (Cal-I-3), whereas Cal-II calcites coexist with zeolite displaying zeolite–calcite veinlets. Geochemically, Cal-I calcites contain relatively high REE(Y) (151–2296 ppm), Sr (4947–9566 ppm) and Na (29–390 ppm) contents, characterized by right- to left-inclined flat distribution patterns [(La/Yb)N = 0.2–4.2] with enrichment of HREE(Y) (136–774 ppm), whereas Cal-II calcites display low REE, Sr and undetectable Na contents, characterized by a right-inclined distribution pattern [(La/Yb)N = 13.5, n = 16]. The U–Nb–REE mineralization, accompanied with intense and extensive fenitization and biotitization, is mainly associated with the Cal-I-3 calcites which show flat to relatively left-inclined flat REE distribution patterns [(La/Yb)N = 0.2–1.0]. Isotopic results show that Cal-I calcites with mantle signatures are primarily igneous in origin, whereas Cal-II are hydrothermal, postdating the U–Nb–REE mineralization. Cal-I calcites (Cal-I-1, Cal-I-2 and Cal-I-3) from mineralized and unmineralized carbonatites, displayed regular changes in REE, Na and Sr contents, but similar trace element distribution patterns and Sr–Nd-C-O isotopic signatures, indicating that these carbonatites originated from the same enriched mantle (EM1) source by low-degree partial melting of HREE-rich carbonated eclogites related to recycled marine sediments. The combination of trace elements and Sr-Nd isotopic composition of calcites further reveals that these carbonatites have undergone highly differentiated evolution. Such differentiation is conducive to the enrichment of ore-forming elements (U–Nb–REE) in the late magmatic–hydrothermal stages owing to extensive ore-forming fluids exsolved from carbonatitic melts. The massive precipitation of the U–Nb–REE minerals from ore-forming hydrothermal fluids may have been triggered by intense fluid–rock reactions indicated by extensive and intense fenitization and biotitization. Therefore, the Huayangchuan carbonatite-related U-Nb-REE deposit may have formed by a combination of processes involving recycled U–Nb–REE–rich marine sediments in the source, differentiation of the produced carbonatitic magmas, and subsequent exsolution of U–Nb–REE–rich fluids that precipitated ore minerals through reactions with wall rocks under the transitional tectonic regime from compression to extension at the end of Late Triassic.