The Miaoya REE deposit associated with carbonatite-syenite complexes is located in the southwestern margin of the Wudang Terrane at the east Qinling orogenic belt. The carbonatite occurs as stocks and principally consists of calcite. The carbonatite-syenite complexes contain abundant REE-rich minerals, and form a large LREE deposit in China. The carbonatite C-O isotopic data are δ18O = 11‰~12.49‰, and δ13C =-3.79‰~5.68‰, which is deviated from primary mantle-derived C-O isotopic compositions, indicating that they were affected by high temperature fractional crystallization. The phases of fluid inclusions are much uniform. Compared with REE deposit of hydrothermal ore-veins in Maoniuping in C-O isotope, fluid inclusions and trace elements, there are different genesis processes. Miaoya carbonatite is typical magmatic REE deposit, which is absent in hydrothermal gangue mineral veins, such as fluorite and so on.