Transmission electron microtomography (TEMT) has proven to be useful for investigating three-dimensional (3D) nanostructures in polymeric systems. However, the conventional TEMT that uses a tilt series around an axis occasionally fails to reconstruct nanostructures, especially when the nanostructure is highly anisotropic. Namely, if a certain geometrical relationship between orientation of the nanostructure and the tilt axis is fulfilled, the nanostructure does not appear in the 3D reconstruction. This problem can be solved by tilting the specimen around two (orthogonal) tilt axes and combining the resulting two 3D reconstructions after precise alignment between them. The strategy, called "dual-axis tomography", is used to observe one of the commonly observed anisotropic polymer nanostructures, cylindrical morphology, of poly(styrene-block-isoprene) block copolymer. It was experimentally observed that the cylindrical nanodomains that were "missing" in one of the two tomograms were complementary reconstructed in the other tomogram obtained from the tilt series using the orthogonal tilt axis to the first data set. Subsequently, the two 3D reconstructions were combined to generate a new 3D reconstruction, in which the cylinders at any orientation were successfully imaged with improved image quality. Although the single-axis tomography gave always lower volume fraction of the cylindrical microdomains than the predicted one calculated on the basis of known molecular composition, an excellent agreement was obtained between the two in the dual-axis tomography. In addition, 3D images taken by the TEMT were shown to be quite effective to determine the nanostructure, i.e., cylindrical structure, which otherwise could be assigned to be lamellar nanostructure by other (surface) observation technique such as AFM or SEM.