This study investigates the hydrogenetic ferromanganese crust (HFMC) from the Magellan Seamounts in the northwest Pacific Ocean, focusing on its mineralogy, crystal chemistry, and paleoclimatic records. Given that ferromanganese is composed of poorly crystalline MnOx phases, such as vernadite, structural determination using conventional X-ray diffraction (XRD) methods is challenging and has very limited effectiveness. Therefore, synchrotron-based pair-distribution function (PDF) analysis of total X-ray scattering and high-resolution electron microscopy techniques were employed to characterize the structures and compositions of HFMC. The results from the synchrotron XRD and transmission electron microscopy (TEM) reveal that the studied HFMC consists primarily of poorly crystalline Fe-bearing vernadite. The chemical analysis of the HFMC layers indicates that the rare-earth elements (REE) and P were preferentially adsorbed on the Fe-rich vernadite, whereas platinum-group elements (PGE), Co, and Ni were enriched in the Mn-rich vernadite. The top layers of the HFMC display fine-scale compositional variations (cycle of ~1600 y) that signify millennial-scale paleoclimate oscillations during the Middle-Late Pleistocene and Holocene periods linked to the glacial termination event that occurred ~126,000 y ago. This millennial-scale oscillation correlates with sea-level variations influenced by the expansion and contraction of ice sheets, offering a crucial signal for understanding the paleoclimatic interpretation throughout the glacial periods. To fully decipher the fine-scale paleoclimate signals and assist in forecasting future climatic conditions, a more extensive examination of ferromanganese crusts from diverse depths, sources, and locations is necessitated.