The rare earth elements (REEs) have unique and diverse properties that make them function as an “industrial vitamin” and thus, many countries consider them as strategically important resources. China, responsible for more than 60% of the world’s REE production, is one of the REE-rich countries in the world. Most REE (especially light rare earth elements (LREE)) deposits are closely related to carbonatite in China. Such a type of deposit may also contain appreciable amounts of industrially critical metals, such as Nb, Th and Sc. According to the genesis, the carbonatite-related REE deposits can be divided into three types: primary magmatic type, hydrothermal type and carbonatite weathering-crust type. This paper provides an overview of the carbonatite-related endogenetic REE deposits, i.e., primary magmatic type and hydrothermal type. The carbonatite-related endogenetic REE deposits are mainly distributed in continental margin depression or rift belts, e.g., Bayan Obo REE-Nb-Fe deposit, and orogenic belts on the margin of craton such as the Miaoya Nb-REE deposit. The genesis of carbonatite-related endogenetic REE deposits is still debated. It is generally believed that the carbonatite magma is originated from the low-degree partial melting of the mantle. During the evolution process, the carbonatite rocks or dykes rich in REE were formed through the immiscibility of carbonate-silicate magma and fractional crystallization of carbonate minerals from carbonatite magma. The ore-forming elements are mainly sourced from primitive mantle, with possible contribution of crustal materials that carry a large amount of REE. In the magmatic-hydrothermal system, REEs migrate in the form of complexes, and precipitate corresponding to changes of temperature, pressure, pH and composition of the fluids. A simple magmatic evolution process cannot ensure massive enrichment of REE to economic values. Fractional crystallization of carbonate minerals and immiscibility of melts and hydrothermal fluids in the hydrothermal evolution stage play an important role in upgrading the REE mineralization. Future work of experimental petrology will be fundamental to understand the partitioning behaviors of REE in magmatic-hydrothermal system through simulation of the metallogenic geological environment. Applying “comparative metallogeny” methods to investigate both REE fertile and barren carbonatites will enhance the understanding of factors controlling the fertility.