A biostratigraphic study on calcareous nannofossils from the CM3D06 Co-rich ferromanganese crust from the Magellan seamounts in the northwestern Pacific enabled estimation of depositional age. The bio-imprinting of calcareous nannofossils and other fossil species suggests six age ranges for the nannofossils: late Cretaceous, late Paleocene, (early, middle, late) Eocene, middle Miocene, late Pliocene, and Pleistocene. Gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS) were used to test the Co-rich crusts, and a variety of molecular fossils were detected, such as chloroform bituminous “A” , n-alkane, isoprenoid and sterol. Peak carbon and molecular indices (such as ΣC23?/ΣC24+, CPI, Pr/Ph, Pr/nC17, Ph/nC18 and δ13C) indicate that the parent organic matter is dominated by marine phytoplankton and thallogen whereas there is little input of terrestrial organic matter. Researches on calcareous nannofossils, molecular fossils and molecular organic geochemistry data reveal that the Paleocene/Eocene (P/E) global event is recorded in the cobalt-rich crusts from the northwestern Pacific Ocean. A succession of biomes can be observed near the 85 mm boundary (about 55 Ma), i.e., the disappearance of the late Cretaceous Watznaueria barnesae and Zigodicus spiralis, and Broisonia parka microbiotas above the P/E boundary, and the bloom of Coccolithus formosus, Discoaster multiradiatus, Discoaster mohleri and Discoaster sp. below the boundary. Typical parameters of molecular fossils, such as saturated hydrocarbon components and carbon-number maxima, Pr/Ph, Pr/C17, Ph/C18, distribution types of sterols, Ts/Tm ratios and bacterial hopane, also exhibit dramatic changes near the P/E boundary. These integrated results illustrate that the biome succession of calcareous nannofossils, relative content of molecular fossils and molecular indices in the cobalt-rich crusts near the 85 mm boundary faithfully record the P/E global event.