In the needle-punching process, barbs of needle catch the fibers and orient it along the thickness direction of fabric. The oriented fibers form a pillar-shaped fiber bundle, which act as a bonding point of fabric. Therefore, the structure of pillar-shaped fiber bundle governs the mechanical properties of needle-punched nonwoven fabric, both of which are largely influenced by needle-punching conditions. However, the three-dimensional (3D) structure of pillar-shaped fiber bundles and its development due to the needle-punching conditions have not been revealed. In this research, we used X-ray micro computed tomography (XCT) and visualized the pillar-shaped fiber bundles by using PET and PE fibers, between which there is a large difference in X-ray absorption rate, then we investigated the 3D structure of pillar-shaped fiber bundles and its development as a function of penetration depth of needle. In the 3D images obtained by XCT, we could clearly observe the 3D structure of pillar-shaped PET fiber bundles by erasing the PE bulk fibers, and the pillar structure developed with the increase of penetration depth of needle. Especially, at the penetration depth of 19.0 mm, the pillars protruded from the bottom surface of fabric and the fibers constituting the pillar were interlocked with the fibers of following pillar with the large increase of the number of fibers constituting a pillar.