The structure and crystal chemistry of vernadite in ferromanganese crusts from the Magellan Seamount in the north-west Pacific Ocean have been investigated using synchrotron X-ray diffraction (XRD), X-ray pair distribution function (PDF) and high-resolution transmission electron microscopy (TEM). XRD patterns of vernadite mainly show two strong diffraction peaks at 2.42–2.43 Å and 1.41 Å without or with a broad (001) diffraction peak, indicating thin layer nanophases along the c-direction. TEM images show flat and curved sheet-like nanocrystals with (001) layer thickness of ∼7.2 Å and ∼9.6 Å, and their interstratified structure. PDF patterns of the vernadite are similar to those from synthetic δ-MnO₂ and defective birnessite, suggesting a phyllomanganate framework. Combined XRD/PDF patterns suggest that vernadite in the outer part is associated with a higher density interlayer species at triple-edge sharing sites. The proportion of the 10 Å phase increases from the outer (young) part to the inner (old) part of the Mn crusts due to aging and sorption of Mn, Co and Ni from ambient seawater. This study suggests that this combined method of synchrotron radiation XRD/PDF and high-resolution TEM is a powerful tool to determine atomic structures of poorly crystallized nano-minerals. The mixture model of vernadite structure will help to understand the partitioning and distribution of trace elements in the ferromanganese crusts.