The high-performance filament yarns, such as carbon fiber yarn, glass fiber yarn, and Kevlar fiber yarn, have characterized as unidirectional,high parallel filament in fiber bundle. However, due to the difficulties in statistically analyzing the micro-structural characteristics of high-performance fiber bundles comprising of thousands of filaments, Nylon (PA6) filament yarns were chosen as the substitute of high-performance fiber bundles to study the deformation micro-mechanisms of fiber bundles under transverse compressive stresses. In order to evaluate the effects of different compressive stresses on the deformation properties, the synchrotron radiation X-ray micro-computed tomography (micro-CT) was used to obtain cross-section images of the fiber bundle during the compression testing. In particular, the influences of compressive stress on the fiber volume fraction, fiber distribution, fiber contact, and fiber orientation were studied. Results indicate a strong dependence of the microstructure of fiber bundles on the compressive stress.