The Magellan Seamounts in the Western Pacific, as an important contract area for ferromanganese crusts exploration, contain high potential of rare earth resources. In this paper, the geochemistry of rare earth elements and yttrium (REY) from 11 top surface ferromanganese crust samples (＜1 mm) collected from the Kocebu Guyot were studied. We analyzed the REY composition characteristics and genetic type of the samples and discussed the factors which control the enrichment of REY. The results show that the average REY abundance (ΣREY) of the crusts is 1366 mg/kg, which is lower than that from other seamounts in Magellan Seamounts and Marcus-Wake Seamounts. The Kocebu Guyot is characterized by enriched light REE and high positive Ce anomalies (mean δCe value 1.45). Genetic discrimination diagram, normalized REY plots and REY partition coefficient patterns indicate that all the crusts are hydrogenetic in origin. REY abundance and dissolved oxygen content in seawater should be regarded as primary environmental parameters controlling the growth of crusts. The lower REY abundance in the samples is related to the water depth and affected by lower REY and oxygen content in shallower waters near Kocebu Guyot, but not observably diluted by detrital minerals. Geochemistry research and resource evaluation of ferromanganese crusts in seamount areas should take the influence of water depth into further consideration, the analysis of samples from limited water depth may cause large deviations in the research results.