The distribution and mechanism of soil aggregates in the source area of the Hanjiang river and Jialing River were studied by experimental and data analysis of soil aggregates and physic-chemical properties. The results showed that:(1) The content of aggregates of >0.25 mm (R_0.25), mean weight diameter (MWD) and geometric mean diameter (GMD) of aggregates in the source area of Hanjiang River decreased from 83.73%, 2.17 and 1.11 of surface layer to 59.18%, 0.40 and 0.26 of parent material layer, respectively, while those of Jialing River decreased from 69.72%, 1.03 and 0.46 of surface layer to 56.55%, 0.52 and 0.27 of parent material layer. While the fractal dimension (D) increased with the depth deepening, and the D of the former increased from 2.46 of surface layer to 2.53 of parent material layer, and those of the latter increased from 2.50 of surface layer to 2.57 of parent material layer, indicating that the stability of soil aggregates decreased with the increases of depth. The >2 mm and 1~2 mm aggregates had important contribution to the stability of soil. (2) Organic matter, iron and aluminum oxides and silt in particle composition were important factors to promote the formation of soil aggregates and maintain their stability, while SiO₂, K₂O, clay, sand and calcium carbonate had the opposite effects on aggregate stability in different soil environments. In other words, the first three factors were unfavorable to the stability of aggregates in LJH profile, but are beneficial to maintain their stability in YJS profile. The last two factors promoted the formation of aggregates in LJH profile, but destroyed the stability of YJS profile. It had a dispersion effect on aggregates after Na₂O dissolved by water. (3) In the source area of Hanjiang River, the stability of aggregates in surface layer was stronger than that in Jialing River source area, and the main factors were silt, organic matter and iron aluminum oxide. The soil mass of leaching layer was dense and weak in permeability, which was unfavorable for the formation of aggregates, and the stability was weaker than the latter. The stability of aggregates of the parent material layer in both places was poor. Besides, the stability difference of soil in the source area of Hanjiang River in different genetic layers was greater than that in the Jialing River.