X-ray microscopy using computed tomography (CT) is an excellent three-dimensional imaging instrument. Three-dimensional X-ray microscopy (3DXRM) is a nondestructive imaging technique used to inspect internal and external structures in units of submicrometers or less. The 3DXRM, although attractive, is mostly used as an observation instrument and is limited as a measurement system in quantitative evaluation and quality control. Calibration is required for use in measurement systems such as coordinate measurement systems, and specific standard samples and evaluation procedures are needed. The certified values of the standard samples must ideally be traceable to the International System of Units (SI). In the 3DXRM measurement system, line structures (LSs) are fabricated as prototype standard samples to conduct magnification calibration. In this study, we evaluated the LS intervals using calibrated cross-sectional scanning electron microscopy (SEM). A comparison of the evaluation results between SEM and 3DXRM for the LS intervals provided the magnification calibration factor for 3DXRM and validated the LSs, whereby the interval methods and feasibility of constructing an SI traceability system were evaluated using the calibrated SEM. Consequently, a magnification calibration factor of 1.01 was obtained for 3DXRM based on the intervals of the LSs evaluated by SEM. A possible route for realizing SI-traceable magnification calibration of 3DXRM has been presented.