The observation of the inner structure of materials without pretreatment or damage is a very useful analytical method in the field of materials science as well as in medicine and biology. We have carried out a three-dimensional (3D) analysis of biodegradable polyester bacterial-poly[(R)-3-hydroxybutyrate-co-(R)-3-hydroxyvalerate] (P(3HB-co-3HV)) fibers with high tensile strength (1.07 GPa) using X-ray microtomography with synchrotron radiation. The inner structure of the fibers was visualized at a spatial resolution of 1 μm. There are many fine voids for one-step-drawn P(3HB-co-3HV) fibers after isothermal crystallization from the result of X-ray microtomography. This revealed that the clear streak reflection along the equator in small-angle X-ray scattering is caused by these fine voids. The recalculated tensile strength of one-step-drawn P(3HB-co-3HV) fibers after isothermal crystallization is suggested to be 2.02 GPa, taking the cross-section area with 52.7%(polymer region) into consideration. These fine voids in fibers seemed to be generated by the volume changes due to the contraction of polymer chains during isothermal crystallization.