A certain type of deep‐sea sediment exhibits very high content of rare earth elements and yttrium (REY) and is therefore expected to serve as a novel resource for these industrially essential metals. In this paper, we statistically analyzed the bulk chemical composition of deep‐sea sediments collected from the western North Pacific Ocean. By applying independent component analysis to the multielemental data set, we extracted three independent components (ICs) that can be interpreted as the influence of Mn‐oxides (IC1), REY‐enriched biogenic calcium phosphate (IC2), and possibly a diagenetic effect involving Cu enrichment (IC3) on bulk sediment geochemistry. Subsequently, we selected representative samples based on the independent component analysis result, and implemented Sr–Nd–Pb isotopic analyses of bulk sediments. The results indicate that the extremely REY‐rich mud characterized by IC2 inherits the geochemical signature of deep Pacific seawater, whereas the non‐REY‐rich mud with less diagenetic alterations, characterized by IC3, implies an influence of terrigenous dust probably from the Taklimakan desert–Chinese loess plateau. IC1 may reflect the variation in sedimentation rates. Characteristic downhole variations of IC1 and IC3 scores imply the presence of hiatus and/or erosion of the sediment column across the REY content peak. The putative cause is an enhanced bottom current, which can physically separate coarse biogenic calcium phosphate grains with very high REY content and thus produce an extremely REY‐enriched sediment layer.