Phosphorite deposit is a kind of marine sedimentary phosphate deposit with the francolite as the main ore mineral. These deposits were formed in the upwelling areas during six historical periods after Paleoproterozoic, and are generally related to the biological activity and the intensity of continental weathering. The formation of phosphorite deposits is controlled by marine transgressions and regressions, microbial activities and physical and chemical conditions of sediment pore water. The key factors for the formation of phosphorite deposits with high rare earth elements (REEs) content are low sedimentation rate and periodic submarine storms. Some phosphorite deposits are rich in medium and heavy REEs, which are potential important REE resources. The main host mineral of REEs in phosphorite is francolite. The REEs in francolite are mainly derived from seawater in sedimentary period and sediment pore water in early diagenetic period, and are incorporated into francolite via adsorption or lattice substitution. REEs can be adsorbed on the surface of marine particles by forming as REEs-carbonate complex and released by the marine particles decomposing that is induced by the change of redox conditions in the sediment pore water. Through the previous research, it is found that different marine particles preferentially adsorb different REEs, which results in the formation of different REEs patterns of pore water and then affects the patterns of francolite in phosphorite deposits. The enrichment of REEs in francolite is equal for light, medium and heavy REEs and different REEs patterns in francolite are derived from contrasting fluid sources. In general, seawater can produce a HREEs-enriched pattern, and pore water might yield a MREEs-bulge pattern (enrichment of medium REEs). As the phosphorite deposits with significant REEs contents are characterized by MREEs-bulge patterns that are consistent with Fe-Mn (oxyhydr)oxides input by the submarine hydrothermal process and the pore water in the early diagenetic process, which may indicates the influence of the submarine hydrothermal activities and the early diagenetic process on the REEs enrichment mechanism of phosphorite deposits. In this paper, the metallogenic process of phosphorite deposits is summarized from the characteristics, spatiotemporal distribution and metallogenic control factors of phosphorite deposits; the enrichment behavior and differentiation behavior of REEs in the process of phosphorite mineralization are analyzed from the content and anomaly of REEs in phosphorite deposits; and the possible enrichment mechanism of REEs in phosphorite rocks with abnormal enrichment of REEs is revealed. The study of metallogenic process and REEs enrichment mechanism of phosphorite deposits is of great significance for the prospecting and exploitation of phosphorite deposits that are highly enriched in REEs.