The change of soil structure under freeze-thaw cycles is one of the main reasons for the aggravation of soil erosion on black soil slope during snowmelt period. The stability and microstructure of soil aggregates are the key factors affecting soil erodibility. Based on the controlled freezing and thawing simulation experiment, the dynamic characteristics of the microstructure of black soil aggregates during the freeze-thaw cycles were analyzed by using the wet sieving method, scanning electron microscopy (SEM) and Image Pro Plus (IPP) analysis. Moreover, the interaction between the water stability and the microstructure characteristics of soil aggregates was elucidated. The results showed that: (1) The destructive effect on soil aggregate stability was found during the freezing and thawing cycles. At the micro level, the freeze-thaw cycles derived soil pores to develop into long strips. With the increase of freeze-thaw cycles, the connectivity of soil pores and the area porosity increased. On the macro level, it showed that soil macro aggregates migrated to micro aggregates, and the water stability of aggregates decreased. (2) The increase of soil initial water content would enhance the damage degree of soil aggregate under freeze-thaw cycles, and there was a significant change within seven freeze-thaw cycles. With the increase of soil initial water content, the aggregate area porosity increased significantly. (3) Aggregate area porosity was significantly correlated to the mean weight diameter (MWD) and the geometric mean diameter (GMD). The increase of area porosity could explain 49.1% and 50.3% of MWD and GMD, respectively.