To clarify the characteristics of soil aggregate breakdown and transportation by rainfall, the cultivated land (0–10 cm) of the black soil region of Northeast China was taken as the research object, with rainfall intensities of 78 and 127 mm·h−1 (RI78, RI127), to analyze the differences in the mass transported, fraction size distribution, mean weight diameter (MWD) and enrichment rate of aggregates before and after runoff generation. Before runoff generation, the total mass of transported aggregates, the total mass percentage of the aggregate fraction size < 1 mm and the MWD of the transported aggregates were not significantly different at rainfall intensities of 78 and 127 mm·h−1. After runoff generation, the mass of transported aggregates was greater than that before runoff generation, and the mass of transported aggregates under RI78 was significantly higher than that under RI127, by 15.6%. The mass percentage of the aggregate fraction size < 0.053 mm after runoff generation was significantly reduced by 8.4% and 19.4% compared to that before runoff generation. After runoff generation, compared with before runoff generation, the MWD of the transported aggregates was significantly reduced by 50.9% and 50.3% under RI78 and RI127, respectively. Compared with before runoff generation, the mass percentage of small macroaggregates increased gradually with the increase in the transport distance. The aggregate fraction size > 0.25 mm was lost, and the fraction size < 0.25 mm was enriched, before and after runoff generation. A comparative study on the characteristics of black soil aggregate breakdown and transportation before and after runoff generation can provide a theoretical basis for the mechanism of soil erosion and the transportation of cultivated soil in the black soil region of Northeast China.