Rare earth elements plus yttrium (REY), well-known critical metals for many new and emerging technologies and as proxies in geological events, are one type of the most important high-tech metals in ferromanganese (Fe-Mn) crusts. The REY(III) are accumulated in Fe-Mn crusts through adsorption by Fe-Mn (oxyhydr)oxides. However, negative correlations between Mn and REY in some Fe-Mn crusts reveal a controversial role of Mn oxides in REY enrichment, which remains equivocal. In this study, texture, structure, mineralogy, and microstratigraphic geochemistry with the growth of a Fe-Mn crust (MP2D32A) from the Line Islands archipelago were analyzed using multiple microanalysis methods. The Fe-Mn crust is characterized by laminar structures, stromatolite-like structures, and micronodules that are primarily composed of low-crystalline Fe-vernadite and ferrihydrite. Throughout the profiles of MP2D32A, the contents of elements are more or less interdependent. Analysis of elemental correlations from the MP2D32A samples and 847 collected data sets from non-phosphatized hydrogenetic Fe-Mn crusts shows Fe plays a positive role and Mn plays multiple roles in REY accumulation during Fe-Mn crust formation. The REY content increases initially and then decreases with increasing Mn content and Mn/Fe ratio and the turning points (i.e., highest REY contents) mainly occur at an Mn content of ∼18–26% and an Mn/Fe content ratio of ∼0.8. These fundamental results provide novel insights into understanding the influence of Fe and Mn in REY accumulation in the Fe-Mn crusts and are very significant in enhancing our understanding of the REY geochemical processes in the ocean.