In Northeast China, seasonal freezing and thawing have been shown to cause significant physical changes in soil. The change in soil microstructure might be attributed to the freeze-thaw action during early spring. The freeze-thaw action affects soil microstructure directly by affecting soil aggregate, which is the basic unit of soil structure. Synchrotron-based X-ray micro-computed tomography can nondestructively capture images of the interior structure with high resolution and strong contrast, and therefore, is an excellent tool to investigate the 3-D microstructure of soil aggregates. Samples of soil aggregates were collected from laboratory freeze-thaw tests with different number of freeze-thaw cycles, and the aggregates were scanned with micro-CT at a resolution of 3.25 μm. The microstructure of aggregates was visualized and quantified by the digital image analysis method using Image J software. The results showed that with the increase in number of freeze-thaw cycles, the soil porosity increased, and the proportion of extended pore and pores > 100 μm also increased. When the number of freeze-thaw cycles was >7, the aggregate porosities increased with the increase in number of freeze-thaw cycles. The results showed that the number of freeze-thaw cycles significantly influenced the structural characteristics of black soil aggregates. This study provides a theoretical basis for the study of freeze-thaw erosion and control of soil erosion during thawing in spring.