This article reports the recent advances in hydrothermally synthesized iron oxide nanoparticles (Fe3O4 NPs) used for magnetic resonance (MR) imaging applications. The hydrothermally synthesized Fe3O4 NPs have a controllable size, narrow size distribution, and tunable magnetic properties. For biomedical imaging applications, the surface-functionalized Fe3O4 NPs with good water dispersibility, colloid stability, and relatively high r(2) relaxivity can be synthesized using modified hydrothermal routes, and can be further surface functionalized with targeting ligands, enabling effective tumor MR imaging with high specificity via receptor-mediated active targeting pathway. What is more, the hydrothermal route can also be used to synthesize Fe3O4@Au composite nanoparticles (CNPs) for dual-mode MR and computed tomography (CT) imaging applications. Some of the key developments in this area of research will be introduced in detail.