Although authigenic pyrite (FeS2) in marine sediment is an important proxy for oxygen conditions and microbial activities at its formation site, very little is known about its morphological characteristics in the deep-sea (> 3500 m) environment and their paleoceanographic implications. Here, we report the occurrence characteristics of authigenic pyrite including texture, size distribution, and relative content in North Atlantic deep-sea sediments from Integrated Ocean Drilling Program (IODP) Expedition 342 Site U1406. The results of electron microscopy show octahedral pyrite microcrystals of 1.5–4.0 μm, the spherical texture of greigite (Fe3S4), and large pyrite framboids (average, 25 μm) relative to those of the continental margin. These features may demonstrate an unchanged supersaturation level of the pore water for octahedral pyrite after its initial formation, replacement of the precursor greigite by pyrite, and an expanded pyrite framboid formation zone with a low sulfate reduction rate in deep-sea sediments, respectively. Although the size distribution of pyrite framboids measured in this study falls into the range of pyrites formed in the sulfate–methane transition zone, based on onboard geochemical data and previous research, these pyrites most likely formed through organoclastic sulfate reduction during diagenesis. We assessed the implications of these findings for paleoceanographic changes, as the formation of diagenetic pyrite is controlled by the supply rate and reactivity of organic matter, which are closely related to ocean productivity and circulation. A comparison between the profiles of relative pyrite content and benthic foraminiferal oxygen isotope (δ18Obf) values indicated that these factors were anti-phased during the late Oligocene. Based on our results, we conclude that the formation of diagenetic pyrite was favored during interglacial periods due to increases in the amount and reactivity of organic matter driven by more energetic formation of proto-North Atlantic Deep Water. Our findings provide new insights into the formation of authigenic pyrite in deep-sea environments and its potential as a paleoceanographic proxy.