Many studies have shown that arbuscular mycorrhizal (AM) fungus has an important role in soil aggregate formation and stabilization. While most studies about the effects of AM fungus on soil aggregate have experimental set-ups in single pots or containers with two compartments, these studies cannot differentiate the effects of roots, mycorrhizal roots or hyphae. In this study we used containers with four compartments to split the roots and quantitatively compare the change of soil aggregate in the mycorrhizosphere soil, rhizosphere soil, hyphosphere soil and bulk soil. Our results demonstrate a significant positive correlation among hyphal length density, easily extractable glomalin (EEG) and aggregate mean weight diameter (MWD), geometric mean diameter (GMD) and percentage of soil macroaggregate with a diameter larger than 0.25 mm (R0.25). The GMD and MWD of R0.25 in the hyphal compartment were higher than those in the non-inoculated root compartment, but were lower than those in the mycorrhizal compartment. This suggests the mycorrhizal hyphae had a greater effect than the non-inoculated roots, but less of an effect than the mycorrhizal roots on the formation and stabilization of soil aggregate. The results reveal that plant roots, mycorrhizal roots and mycorrhizal hyphae contribute to aggregate stability in individual ways and that their effects are additive, creating a synergistic stabilizing effect.