Background and aims <p>Intercropping increases soil aggregate stability, and the associated microbial and botanical mechanisms have been thoroughly explored. However, the response of aggregate stability to soil colloids that are key factors mediating soil aggregation remains unclear in intercropping.</p> Methods <p>An intercropping field experiment was conducted in northwest China in 2009. The relationship between soil aggregates and soil colloids were investigated at 12th and 13th year of continuous faba bean/maize and oilseed rape/maize intercropping and corresponding crop monocultures.</p> Results <p>Intercropping significantly increased the proportion of &gt; 2&#xa0;mm aggregates by 37.1–59.2% and enhanced aggregate stability while decreasing the contents of 0.25–2&#xa0;mm and &lt; 0.25&#xa0;mm aggregates compared with the corresponding monocultures. Intercropping also increased fulvic acid content in organic colloids by 4.4–5.7% and decreased free Fe oxide, amorphous Fe, and Al oxide contents in inorganic colloids, compared to corresponding crop monocultures. A decrease in the absolute value of the zeta potential and altered stability behaviors of soil colloids indicate that intercropping destabilizes soil colloids, promoting their coagulation. The fulvic acid content was positively correlated with, but the absolute value of the zeta potential was negatively correlated with &gt; 2&#xa0;mm aggregate contents.</p> Conclusion <p>Intercropping effectively increases the proportion of soil large macro-aggregates (&gt; 2&#xa0;mm) and enhance overall aggregate stability, largely through its regulation of soil colloid properties. The increased fulvic acid content and reduced electrostatic stability of soil colloid induced by long-term intercropping contribute to promote particles flocculation and aggregate formation in intercropping.</p>