Carbon fiber (CF)/pyrolytic graphite (PG) composites are promising structural materials for molten salt reactors because of their superior performance. Due to the minor density difference between CF and PG, existing methods are impractical for efficient three-dimensional characterization of CF/PG composites. Therefore, in this study, a method based on in-line phase-contrast X-ray microtomography was developed to solve the aforementioned problem. Experimental results demonstrate that the method is suitable for comprehensive characterization of CF/PG composites. The relationship between the microporous defects and fiber orientations of such composites was also elucidated. The findings can be useful for improving the manufacturing process of CF/PG composites.