Bioapatite (i.e., fish teeth and debris) is considered the predominating carrier of rare earth elements (REY, including lanthanide (Ln) and yttrium (Y)) due to the positive correlation between phosphorus (P) and REY in REY-rich deep-sea sediments. Besides bioapatite, the presence of various P species such as vivianite and authigenic carbonate-fluorapatite suggests other P species may have also contributed to the enrichment of REY in the REY-rich deep-sea sediments, yet their roles in REY enrichment are still unclear. This study investigated the REY characteristics of five P species (fractions), including exchangeable and loosely adsorbed P (Ex-P), Fe oxides bound P (Fe-P), authigenic apatite, and biogenic apatite (Ca-P), detrital apatite (Detrital-P), and organic-P (Org-P), in deep-sea sediments from the Pacific Ocean by using the sedimentary extraction (SEDEX) method and micro-scale analysis. The results show that Ca-P contributes 49.42% of the total P, while Fe-P and Detrital-P comprise 45.04% of the total P. The heavy rare earth enrichment is more visible in Fe-P and Ca-P compared to insignificant trends in the other fractions. Meanwhile, multiple forms of apatite demonstrate varied sources of REY in the Ca-P fraction. For instance, the formation of new apatite on the surface of a phillipsite explains the exceptionally high REY content in the Ca-P fraction. These results suggest that all investigated P fractions in deep-sea sediments positively contribute to REY enrichment and that in addition to fish teeth, other types of biogenic and authigenic apatites may also be important REY carriers.