Tracking of cells in biological systems is critically important for monitoring disease treatment, such as in stem cell therapy. This report prepared new types of biocompatible gadolinium hybrid iron oxide (GdIO) nanocomposites, which demonstrated high sensitivity for dual T1- and T2-weighted magnetic resonance imaging (MRI). The GdIO nanocomposites could efficiently label mesenchymal stem cells (MSCs) by incubation for 24 h at a safe dose, as they did not affect the cell viability, proliferation or differentiation capacity. There was high contrast enhancement in the GdIO-labeled stem cells for dual T1- and T2-weighted MR imaging. In addition, the GdIO nanocomposites were injected into adult mouse lateral ventricles, where cells could be labeled to monitor their biological behaviors by MRI. These GdIO nanocomposites with dual-imaging functions are a good platform for cell labeling and other diagnostic applications.