Three-dimensional (3D) morphology of a polymer/clay nanocomposite, an organophilic montmorillonite (MMT) dispersed in poly(ethylene-co-vinylacetate) (EVA), was examined by transmission electron microtomography (TEMT). Using this technique, individual clay layers dispersed in the EVA matrix were clearly visualized. A volume fraction of the clay layers evaluated from the 3D reconstructed image agreed well with that calculated from the weight of the MMT component in the MMT/EVA system. The individual clay layers were digitally extracted by a newly developed 3D particle algorithm. A size distribution of the clay layers was directly obtained from the 3D reconstruction. Anisotropy of each clay layer was characterized by the determination of three semi-axes of an approximating ellipsoid with the same volume. One of the representative semi-axis of the ellipsoid was used to estimate average orientation of the MMT layers in the ultra-thin section used in the TEMT experiment. Thus, the combination of quantitative TEMT and 3D structural analysis is shown to be a powerful tool to investigate a relationship between the MMT distribution and a variety of physical properties of the nanocomposites.