Controlled synthesis of monodisperse iron oxide (IO) nanostructures with diverse morphology remains a major challenge. In this work, IO nanostructures with various shapes and surface structures were synthesized by thermal decomposition of iron oleate (FeOL) in the presence of sodium oleate (NaOL). In a mild condition using 1-octadecene (ODE) as solvent, NaOL may preferentially bind to Fe3O4{111} facets and lead to the formation of Fe3O4{111} facets exposed IO plates, truncated octahedrons, and tetrahedrons. While in a high-boiling temperature tri-n-octylamine (TOA) solvent, we obtained Fe3O4{100} facets exposed IO cubes, concaves, multi-branches, and assembled structures by varying the molar ratios of NaOL/FeOL. Moreover, we demonstrated that IO nanoparticles (NPs) with metal-exposed surface structures have enhanced T1 relaxation time shortening effects to protons, and IO NPs with anisotropic shapes are superior in protons T2 relaxation shortening due to the larger effective radii comparing to that of spherical IO NPs. This study can provide rational design considerations to the syntheses and applications of IO nanostructures for a broad community of material research fields.