Phosphorite-type rare earth deposits, which are one of the important types of rare earth elements (REE) ore deposits, have attracted increasing attention because of the extreme enrichments in heavy rare earth elements (HREE), including Yttrium (Y). In this study, in situ geochemical analyses of apatite grains from Zhijin phosphorites were conducted using electron probe microanalysis (EMPA) and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). Based on EPMA mapping analysis, we show that rare earth elements and Yttrium (REY) entering into the crystal lattice by isomorphism rather than by inclusions of REY-bearing accessory minerals. The post-Archean Australian Shales (PAAS)-normalized REY patterns of the apatite grains are characterized by hat-shaped MREE-enriched patterns. We interpret that this pattern may reflect the REE distribution of seawater at that time. We propose that in a local, reducing environment, dramatically increased the concentration of REY in seawater, and resulted in the MREE-enriched patterns in the ancient ocean. The main mechanism for the genesis of the Zhijin phosphorite deposit is the apatite crystallizes during the mixing process of REY- and P-rich fluid and oxidizing seawater.