The Qinling Orogenic Belt (Central China) is a world-class rare earth element (REE) metallogenic belt in which REE deposits are mainly hosted by alkaline rocks and/or carbonatites. The newly discovered Yangyugou REE deposit, hosted by alkaline complexes in this belt, is unusual because the REE mineralization mainly takes the form of Ba- and REE-bearing minerals, such as barytocalcite. In this study, we present whole-rock major and trace elements, zircon geochronology, Hf isotopes, and mineral geochemistry to investigate the enrichment of REE and Ba and origin of this deposit. The REE-bearing alkaline complex at the Yangyugou deposit consists of syenite and carbonatite. Carbonatite exhibits higher concentrations of REE and Ba compared to syenite. The concentrations of REE and BaO in the carbonatite can be up to 6214 ppm and 22.4 wt%, respectively, and exhibit a positive correlation. The carbonatite contains numerous Ba-rich minerals, primarily comprising barytocalcite and a smaller amount of bazirite. The REE concentrations of barytocalcite range from 3059 to 10032 ppm, and the Ba concentration can be as high as 37.4 wt%. The barytocalcite is the primary carrier of REE and Ba in the Yangyugou carbonatite. Zircons from the syenite have a 206Pb/238U weighted mean age of 438.9 ± 3.3 Ma (MSWD = 1.08). The εHf(t) values of these zircons range from −8.28 to −3.17, with two-stage Hf model ages of 1.61–1.93 Ga. Apatite from the syenite has initial 87Sr/86Sr ratios of 0.70906 to 0.70984. Our study indicates that syenite-carbonatite complex was probably derived from the enriched mantle that has been metasomatized by a Ba-rich fluid, and that the early Silurian alkaline magmatism may be related to the opening of the Erlangping back-arc basin.