The aggregation behavior of the newly synthesized gadofullerene magnetic resonance imaging (MRI) contrast agent, i.e., Gd@C82O6(OH)(16)(NHCH2CH2COOH)(8) (abbreviated as AAD-EMF), was studied in detail by dynamic light scattering, scanning electron microscopy, T-1-weighted magnetic resonance, and atomic force microscopy. It was revealed that the AAD-EMF aggregation in aqueous solution is pH-dependent. At pH 2, the AAD-EMF first self-assemble to form ca. 30 nm small clusters, and then dozens of the small clusters further aggregate to form large grapelike particles. At pH 7, the aggregates are also ca. 30 nm small clusters, but they are hard to further aggregate except for forming some cluster dimers or trimers, so AAD-EMF aggregates have a narrow size distribution by this time. At pH 9, the AAD-EMF aggregations cover a large range of continuous hydrodynamic diameters from 30 to 2000 nm. On the basis of the above observations, the aggregating mechanism of AAD-EMF under different pH values was proposed by concurrently considering the hydrogen-bonding effect and the dipolar interactions between AAD-EMF.