The development of fluorescent iron oxide nanomaterials is highly desired for multimodal molecular imaging. Instead of incorporating fluorescent dyes on the surface of iron oxides, a ligand-assisted synthesis approach is developed to allow near-infrared (NIR) fluorescence in Fe3O4 nanostructures. Using a trimesic acid (TMA)/citrate-mediated synthesis, fabricated Fe3O4 nanostructures can generate a NIR two-photon florescence (TPF) peak around 700 nm under the excitation by a 1230-nm femtosecond laser. By tailoring the absorption of Fe3O4 nanostructures toward NIR band, the NIR-TPF efficiency can be greatly increased. Through internal etching, surface peeling, and ligand replacement, spectroscopic results validated that such resonantly enhanced NIR-TPF is mediated by surface states with strong NIR-IR absorption. This TPF signal evolution can be generalized to other iron oxide nanomaterials like magnetite nanoparticles and α-Fe2O3 nanoplates. Using the developed fluorescent Fe3O4 nanostructures, it is demonstrated that their TPF and third harmonic generation (THG) contrast in the nonlinear optical microscopy of live cells. It is anticipated that the synthesized NIR photofunctional Fe3O4 will serve as a versatile platform for dual-modality magnetic resonance imaging (MRI) as well as a magnet-guided theranostic agent.