The superparamagnetic magnetite nanoparticles have broad application prospects in the diagnosis and treatment of cancer. Herein, a series of monodispersed exceptionally small-sized superparamagnetic magnetite nanoparticles (ESM NPs) with tunable size were synthesized through thermal decomposition of an iron precursor by simply changing the reaction temperature and stabilizing agents. The underlying mechanisms of regulating the size and properties of ESM NPs were studied. The surface of hydrophobic ESM NPs was modified with a carboxyl-polyethylene glycol-phosphoric acid ligand, and the obtained water-soluble ESM NPs showed extremely high long-term stability under various aqueous environments and physiological conditions. The hemolysis and cytotoxicity evaluations showed that the ESM NPs had good blood compatibility and no obvious cytotoxicity. The 2.3 nm ESM NPs exhibited an extremely high longitudinal relaxivity (r1) of 6.0 mM-1 s-1, which was higher than that of the clinical gadolinium complex contrast agent (r1 = 3.8 mM-1 s-1), and had an appropriate r2/r1 ratio of 4.0. The in vivo results showed that the nanoparticles exhibited superior contrast effects in both T1 and T2 MR imaging, as well as high-resolution contrast in MR angiography. This study provides a general strategy for the controlled synthesis of ESM NPs and reveals the size and property regulation mechanisms, which undoubtedly provides the possibility of designing highly sensitive MR imaging probes based on small-sized magnetic nanoparticles for clinical diagnostic applications.