Marine hydrogenetic Fe–Mn crusts on seamounts are known as potential mineral resources of rare earth elements plus yttrium (REY). In recent years, increasing numbers of deposits of Fe–Mn crusts and nodules were discovered in the South China Sea (SCS), yet the enrichment mechanism of REY is yet to be sufficiently addressed. In this study, hydrogenetic Fe–Mn crusts from the South China Sea (SCS) and the Western Pacific Ocean (WPO) were comparatively studied with mineralogy and geochemistry. In addition, we used an in situ REY distribution mapping method, implementing laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and a sequential leaching procedure to investigate the partitioning behavior of REY in the Fe–Mn crusts. The typical Fe–Mn crusts from SCS were mainly composed of quartz, calcite, vernadite (δ-MnO2), and amorphous Fe oxides/hydroxides (FeOOH). The Fe–Mn crusts from the Central SCS Basin and the WPO contained quartz, δ-MnO2, FeOOH, todorokite, and phillipsite. Furthermore, geochemical analysis indicated that the typical SCS crusts had a higher growth rate and lower REY concentrations. The LA-ICP-MS mapping results showed that the δ-MnO2 and FeOOH dominated the occurrence phases of REY in the SCS crusts. Four mineral phases (i.e., easily exchangeable and carbonate, Mn-oxide, amorphous FeOOH, and residual aluminosilicates) in these Fe–Mn crusts were separated by a sequential leaching procedure. In the SCS and WPO crusts, the majority of total REY (ΣREY) was distributed in the Mn-oxide and amorphous FeOOH phases. The post-Archean Australian shale-normalized REY patterns showed that light REY (LREY) and heavy REY (HREY) were preferentially adsorbed onto δ-MnO2 and FeOOH, respectively. It is noteworthy that ~27% of ΣREY was associated with the residual aluminosilicates phase of the WPO crusts. The La/Al ratios in the aluminosilicates phase of the typical SCS crusts were the values of the upper crust. We conclude that large amounts of terrigenous materials dilute the abundance of REY in the SCS crusts. In addition, the growth rates of Fe–Mn crusts have a negative correlation with the FeOOH-bound and aluminosilicate-bound REY. As a result of the fast growth rates, the SCS crusts contain relatively low concentrations of REY.