Precise diagnosis by magnetic resonance imaging (MRI) requires sensitive magnetic resonance probes to detect low concentrations of magnetic substances. Ionic magnetic clusters (IMCs) as versatile magnetic probes were successfully synthesized for enhancing the magnetic resonance (MR) contrast effect as well as ensuring high water solubility. IMCs with various sizes were prepared by assembly of MNCs using cationic cetyltrimethylammonium bromide (CTAB) and anionic sodium dodecyl sulfate (SDS). To synthesize IMCs in the aqueous phase, magnetic nanocrystals in an organic solvent were assembled with CTAB and SDS using the nanoemulsion method, to fabricate cationic magnetic clusters (CMCs) and anionic magnetic clusters (AMCs), respectively. IMCs demonstrated ultrasensitivity by MR imaging and sufficient magnetic mobility under an external magnetic field.