In order to maintain soil stability, improve soil productivity and optimize planting patterns, the distribution characteristics of soil aggregates in sugarcane fields under different intercropping methods were studied. We investigated the differences in organic carbon content of different particle size aggregates and the effects of intercropping on soil organic carbon, aggregates stability, sugarcane water content and nutrients content. The results showed that intercropping could effectively improve soil physicochemical properties, increase soil organic carbon (SOC) content, but such an approach had little effect on soil stability. After intercropping, the content of SOC, readily oxidized organic carbon (ROC), dissolved organic carbon (DOC) in soil increased significantly. The content of SOC increased with the decrease in aggregate size, and the organic carbon is more stable in the aggregates with the particle size of R>2 mm and R<0.154 mm. The selection of soybean and mucuna pruriens as intercropping crops in both OS//M and OM treatments was less damaging to soil stability and soil performance was significantly improved than the other groups, making them more suitable for intercropping in sugarcane fields. Intercropping increased the water content and N, P and K content of sugarcane plants.